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  <H5 align="left" style="page-break-before:always"><A HREF="#toc">Table of Contents</A></H5><P>
  <DIV style="font-family: 'Times New Roman',Times,serif">
  
  <DIV align="center" style="font-size: 10pt; margin-top: 12pt">As filed with the Securities and Exchange Commission on November&nbsp;14, 2006</DIV>
  
  
  <DIV align="right" style="font-size: 10pt; margin-top: 12pt">REGISTRATION NO. 333 -
  </DIV>
  
  
  <DIV style="width: 100%; border-bottom: 2pt solid black; font-size: 1pt; margin-top: 6pt">&nbsp;</DIV>
  <DIV style="width: 100%; border-bottom: 1pt solid black; font-size: 1pt">&nbsp;</DIV>
  
  
  
  
  <DIV align="center" style="font-size: 14pt; margin-top: 12pt"><B>UNITED STATES SECURITIES AND EXCHANGE COMMISSION</B>
  </DIV>
  
  <DIV align="center" style="font-size: 12pt"><B>WASHINGTON, D.C. 20549</B>
  </DIV>
  
  <DIV align="center" style="font-size: 10pt; margin-top: 12pt"><DIV align="center"><DIV style="font-size: 3pt; margin-top: 16pt; width: 26%; border-top: 1px solid #000000">&nbsp;</DIV></DIV></DIV>
  
  <DIV align="center" style="font-size: 18pt; margin-top: 12pt"><B>FORM S-8</B>
  </DIV>
  
  
  <DIV align="center" style="font-size: 12pt; margin-top: 0pt"><B>REGISTRATION STATEMENT<BR>
  under the<BR>
  SECURITIES ACT OF 1933</B>
  </DIV>
  
  <DIV align="center" style="font-size: 10pt; margin-top: 12pt"><DIV align="center"><DIV style="font-size: 3pt; margin-top: 16pt; width: 26%; border-top: 1px solid #000000">&nbsp;</DIV></DIV></DIV>
  
  <DIV align="center" style="font-size: 24pt; margin-top: 12pt"><B>EPIX Pharmaceuticals, Inc.</B>
  </DIV>
  
  <DIV align="center" style="font-size: 10pt">(<I>Exact Name of Registrant as Specified in Its Charter)</I></DIV>
  
  
  <DIV align="center">
  <TABLE style="font-size: 10pt" cellspacing="0" border="0" cellpadding="0" width="100%">
  <!-- Begin Table Head -->
  <TR valign="bottom">
      <TD width="47%">&nbsp;</TD>
      <TD width="5%">&nbsp;</TD>
      <TD width="47%">&nbsp;</TD>
  </TR>
  <!-- End Table Head -->
  <!-- Begin Table Body -->
  <TR valign="bottom">
      <TD align="center" valign="top"><B>Delaware</B><BR>
  (<I>State or Other Jurisdiction <BR>
  of Incorporation or Organization</I>)
  </TD>
      <TD>&nbsp;</TD>
      <TD align="center" valign="top"><B>04-3030815</B><BR>
  (<I>I.R.S. Employer<BR>
  Identification No.</I>)</TD>
  </TR>
  <!-- End Table Body -->
  </TABLE>
  </DIV>
  
  
  <DIV align="Center" style="font-size: 10pt; margin-top: 6pt"><B>4 Maguire Road<BR>
  Lexington, Massachusetts 02421</B><BR>
  (<I>Address, Including Zip Code, of Principal Executive Offices</I>)
  
  </DIV>
  
  <DIV align="Center" style="font-size: 10pt; margin-top: 6pt"><B>PREDIX PHARMACEUTICALS HOLDINGS, INC.<BR>
  AMENDED AND RESTATED 2003 STOCK INCENTIVE PLAN</B>
  
  </DIV>
  
  <DIV align="Center" style="font-size: 10pt; margin-top: 6pt"><B>PHYSIOME SCIENCES, INC. 1997 STOCK OPTION PLAN</B><BR>
  <I>(Full Titles of the Plan)</I>
  
  </DIV>
  
  <DIV align="center" style="font-size: 10pt; margin-top: 18pt"><B>Michael G. Kauffman, M.D., Ph.D.<BR>
  Chief Executive Officer<BR>
  EPIX Pharmaceuticals, Inc.<BR>
  4 Maguire Road<BR>
  Lexington, Massachusetts 02421<BR>
  (781)&nbsp;761-7600</B><BR>
  (<I>Name, Address and Telephone Number, Including<BR>
  Area Code, of Agent For Service</I>)
  </DIV>
  
  
  <DIV align="Center" style="font-size: 10pt; margin-top: 6pt"><B><I>with copies to:</I></B>
  
  </DIV>
  
  <DIV align="Center" style="font-size: 10pt; margin-top: 6pt"><B>Edward A. King, Esq.<BR>
  Goodwin Procter LLP<BR>
  Exchange Place<BR>
  Boston, Massachusetts 02109<BR>
  (617)&nbsp;570-1000</B>
  
  </DIV>
  
  <DIV align="Center" style="font-size: 10pt; margin-top: 6pt"><B>CALCULATION OF REGISTRATION FEE</B>
  
  </DIV>
  <DIV align="center">
  <TABLE style="font-size: 10pt" cellspacing="0" border="0" cellpadding="0" width="100%">
  <!-- Begin Table Head -->
  <TR valign="bottom" style="font-size: 1pt">
      <TD width="1%">&nbsp;</TD>
      <TD width="24%">&nbsp;</TD>
      <TD width="2%">&nbsp;</TD><!-- VRule -->
      <TD width="2%">&nbsp;</TD>
      <TD width="7%">&nbsp;</TD>
      <TD width="2%">&nbsp;</TD><!-- VRule -->
      <TD width="2%">&nbsp;</TD>
      <TD width="3%">&nbsp;</TD>
      <TD width="1%">&nbsp;</TD>
      <TD width="3%">&nbsp;</TD>
      <TD width="2%">&nbsp;</TD><!-- VRule -->
      <TD width="2%">&nbsp;</TD>
      <TD width="3%">&nbsp;</TD>
      <TD width="1%">&nbsp;</TD>
      <TD width="3%">&nbsp;</TD>
      <TD width="2%">&nbsp;</TD><!-- VRule -->
      <TD width="2%">&nbsp;</TD>
      <TD width="3%">&nbsp;</TD>
      <TD width="1%">&nbsp;</TD>
      <TD width="3%">&nbsp;</TD>
      <TD width="1%">&nbsp;</TD>
  </TR><TR style="font-size: 1px" valign="bottom">
      <TD nowrap align="left" colspan="21" style="border-bottom: 3px double #000000">&nbsp;</TD>
  </TR>
  <TR style="font-size: 8pt" valign="bottom">    <TD width="1%">&nbsp;</TD>
  
      <TD>&nbsp;</TD>
      <TD style="border-right: 2px solid #000000">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD style="border-right: 2px solid #000000">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD nowrap align="center" colspan="3">Proposed</TD>
      <TD style="border-right: 2px solid #000000">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD nowrap align="center" colspan="3">Proposed</TD>
      <TD style="border-right: 2px solid #000000">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD nowrap align="center" colspan="3">&nbsp;</TD>
      <TD width="1%">&nbsp;</TD>
  </TR>
  <TR style="font-size: 8pt" valign="bottom">    <TD width="1%">&nbsp;</TD>
  
      <TD>&nbsp;</TD>
      <TD style="border-right: 2px solid #000000">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD style="border-right: 2px solid #000000">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD nowrap align="center" colspan="3">Maximum</TD>
      <TD style="border-right: 2px solid #000000">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD nowrap align="center" colspan="3">Maximum</TD>
      <TD style="border-right: 2px solid #000000">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD nowrap align="center" colspan="3">&nbsp;</TD>
      <TD width="1%">&nbsp;</TD>
  </TR>
  <TR style="font-size: 8pt" valign="bottom">    <TD width="1%">&nbsp;</TD>
  
      <TD nowrap align="center">Title of</TD>
      <TD style="border-right: 2px solid #000000">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD nowrap align="center">Amount to be</TD>
      <TD style="border-right: 2px solid #000000">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD nowrap align="center" colspan="3">Offering Price</TD>
      <TD style="border-right: 2px solid #000000">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD nowrap align="center" colspan="3">Aggregate</TD>
      <TD style="border-right: 2px solid #000000">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD nowrap align="center" colspan="3">Amount of</TD>
      <TD width="1%">&nbsp;</TD>
  </TR>
  <TR style="font-size: 8pt" valign="bottom">    <TD width="1%">&nbsp;</TD>
  
      <TD nowrap align="center">Securities to be Registered</TD>
      <TD style="border-right: 2px solid #000000">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD nowrap align="center">Registered<SUP style="font-size: 85%; vertical-align: text-top">(1)</SUP></TD>
      <TD style="border-right: 2px solid #000000">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD nowrap align="center" colspan="3">Per Share<SUP style="font-size: 85%; vertical-align: text-top">(2)</SUP></TD>
      <TD style="border-right: 2px solid #000000">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD nowrap align="center" colspan="3">Offering Price</TD>
      <TD style="border-right: 2px solid #000000">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD nowrap align="center" colspan="3">Registration Fee</TD>
      <TD width="1%">&nbsp;</TD>
  </TR>
  
  <!-- End Table Head -->
  <!-- Begin Table Body -->
  <TR valign="bottom">
      <TD width="1%" style="border-top: 2px solid #000000">&nbsp;</TD>
                      <TD style="border-top: 2px solid #000000"><DIV style="margin-left:15px; text-indent:-15px">Common Stock, $0.01 par value</DIV></TD>
      <TD style="border-right: 2px solid #000000; border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD align="center" valign="top" style="border-top: 2px solid #000000"><FONT style="white-space: nowrap">1,116,959 shares</FONT></TD>
      <TD style="border-right: 2px solid #000000; border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD align="right" style="border-top: 2px solid #000000">$</TD>
      <TD align="right" style="border-top: 2px solid #000000">4.21</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-right: 2px solid #000000; border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD align="right" style="border-top: 2px solid #000000">$</TD>
      <TD align="right" style="border-top: 2px solid #000000">4,702,397.39</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-right: 2px solid #000000; border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-top: 2px solid #000000">503.16</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD width="1%" style="border-top: 2px solid #000000">&nbsp;</TD>
  </TR>
  <TR valign="bottom">
      <TD width="1%" style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-top: 2px solid #000000"><DIV style="margin-left:15px; text-indent:-15px">Common Stock, $0.01 par value</DIV></TD>
      <TD style="border-right: 2px solid #000000; border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD align="center" valign="top" style="border-top: 2px solid #000000">1,191,370 shares</TD>
      <TD style="border-right: 2px solid #000000; border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD align="right" style="border-top: 2px solid #000000">$</TD>
      <TD align="right" style="border-top: 2px solid #000000">0.98</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-right: 2px solid #000000; border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD align="right" style="border-top: 2px solid #000000">$</TD>
      <TD align="right" style="border-top: 2px solid #000000">1,167,542.60</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-right: 2px solid #000000; border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-top: 2px solid #000000">124.93</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD width="1%" style="border-top: 2px solid #000000">&nbsp;</TD>
  </TR>
  <TR valign="bottom">
      <TD width="1%" style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-top: 2px solid #000000"><DIV style="margin-left:15px; text-indent:-15px">Common Stock, $0.01 par value</DIV></TD>
      <TD style="border-right: 2px solid #000000; border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD align="center" valign="top" style="border-top: 2px solid #000000">264,139 shares</TD>
      <TD style="border-right: 2px solid #000000; border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD align="right" style="border-top: 2px solid #000000">$</TD>
      <TD align="right" style="border-top: 2px solid #000000">1.74</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-right: 2px solid #000000; border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD align="right" style="border-top: 2px solid #000000">$</TD>
      <TD align="right" style="border-top: 2px solid #000000">459,601.86</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-right: 2px solid #000000; border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;&nbsp;49.18</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD width="1%" style="border-top: 2px solid #000000">&nbsp;</TD>
  </TR>
  <TR valign="bottom">
      <TD width="1%" style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-top: 2px solid #000000"><DIV style="margin-left:15px; text-indent:-15px">Common Stock, $0.01 par value</DIV></TD>
      <TD style="border-right: 2px solid #000000; border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD align="center" valign="top" style="border-top: 2px solid #000000">139,049 shares</TD>
      <TD style="border-right: 2px solid #000000; border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD align="right" style="border-top: 2px solid #000000">$</TD>
      <TD align="right" style="border-top: 2px solid #000000">2.18</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-right: 2px solid #000000; border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD align="right" style="border-top: 2px solid #000000">$</TD>
      <TD align="right" style="border-top: 2px solid #000000">303,126.82</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-right: 2px solid #000000; border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;&nbsp;32.43</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD width="1%" style="border-top: 2px solid #000000">&nbsp;</TD>
  </TR>
  <TR valign="bottom">
      <TD width="1%" style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-top: 2px solid #000000"><DIV style="margin-left:15px; text-indent:-15px">Common Stock, $0.01 par value</DIV></TD>
      <TD style="border-right: 2px solid #000000; border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD align="center" valign="top" style="border-top: 2px solid #000000">3,710 shares</TD>
      <TD style="border-right: 2px solid #000000; border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD align="right" style="border-top: 2px solid #000000">$</TD>
      <TD align="right" style="border-top: 2px solid #000000">2.28</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-right: 2px solid #000000; border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD align="right" style="border-top: 2px solid #000000">$</TD>
      <TD align="right" style="border-top: 2px solid #000000">8,458.80</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-right: 2px solid #000000; border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;&nbsp;&nbsp;&nbsp;0.91</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD width="1%" style="border-top: 2px solid #000000">&nbsp;</TD>
  </TR>
  <TR valign="bottom">
      <TD width="1%" style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-top: 2px solid #000000"><DIV style="margin-left:15px; text-indent:-15px">Common Stock, $0.01 par value</DIV></TD>
      <TD style="border-right: 2px solid #000000; border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD align="center" valign="top" style="border-top: 2px solid #000000">160,306 shares</TD>
      <TD style="border-right: 2px solid #000000; border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD align="right" style="border-top: 2px solid #000000">$</TD>
      <TD align="right" style="border-top: 2px solid #000000">3.62</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-right: 2px solid #000000; border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD align="right" style="border-top: 2px solid #000000">$</TD>
      <TD align="right" style="border-top: 2px solid #000000">580,307</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-right: 2px solid #000000; border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;&nbsp;62.09</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD width="1%" style="border-top: 2px solid #000000">&nbsp;</TD>
  </TR>
  <TR valign="bottom">
      <TD width="1%" style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-top: 2px solid #000000"><DIV style="margin-left:15px; text-indent:-15px">Common Stock, $0.01 par value</DIV></TD>
      <TD style="border-right: 2px solid #000000; border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD align="center" valign="top" style="border-top: 2px solid #000000">17,772 shares</TD>
      <TD style="border-right: 2px solid #000000; border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD align="right" style="border-top: 2px solid #000000">$</TD>
      <TD align="right" style="border-top: 2px solid #000000">6.53</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-right: 2px solid #000000; border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD align="right" style="border-top: 2px solid #000000">$</TD>
      <TD align="right" style="border-top: 2px solid #000000">116,051.16</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-right: 2px solid #000000; border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;&nbsp;12.42</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD width="1%" style="border-top: 2px solid #000000">&nbsp;</TD>
  </TR>
  <TR valign="bottom">
      <TD width="1%" style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-top: 2px solid #000000"><DIV style="margin-left:15px; text-indent:-15px">Total</DIV></TD>
      <TD style="border-right: 2px solid #000000; border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD align="center" valign="top" style="border-top: 2px solid #000000">2,893,305 shares</TD>
      <TD style="border-right: 2px solid #000000; border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD align="right" style="border-top: 2px solid #000000">N/A</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-right: 2px solid #000000; border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD align="right" style="border-top: 2px solid #000000">$</TD>
      <TD align="right" style="border-top: 2px solid #000000">7,337,486.35</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-right: 2px solid #000000; border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD align="left" nowrap style="border-top: 2px solid #000000">$</TD>
      <TD align="right" style="border-top: 2px solid #000000">785.11</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD width="1%" style="border-top: 2px solid #000000">&nbsp;</TD>
  </TR>
  <TR style="font-size: 1px" valign="bottom">
      <TD nowrap align="left" colspan="21" style="border-top: 3px double #000000">&nbsp;</TD>
  </TR>
  
  <!-- End Table Body -->
  </TABLE>
  </DIV>
  
  
  <DIV align="left">
  <DIV style="font-size: 3pt; margin-top: 3pt; width: 18%; border-top: 0px solid #000000">&nbsp;</DIV>
  </DIV>
  
  <TABLE width="100%" border="0" cellpadding="0" cellspacing="0" style="font-size: 10pt">
  <TR>
      <TD width="3%"></TD>
      <TD width="1%"></TD>
      <TD width="96"></TD>
  </TR>
  
  <TR valign="top">
      <TD nowrap align="left">(1)</TD>
      <TD>&nbsp;</TD>
      <TD>The number of shares of common stock, par value $0.01 per share (&#147;Common Stock&#148;), stated
  above consists of the aggregate number of shares which may be sold upon (i)&nbsp;the exercise of
  options which have been granted or upon the exercise of options or issuance of stock awards
  which may hereafter be granted under the Predix Pharmaceuticals Holdings, Inc. Amended and
  Restated 2003 Stock Incentive Plan (the &#147;2003 Plan&#148;), and (ii)&nbsp;the exercise of options which
  have been granted under the Physiome Sciences, Inc. 1997 Stock Option Plan, as amended (the
  &#147;1997 Plan&#148;) which plans were assumed by the Registrant on August&nbsp;16, 2006, pursuant to an
  Agreement and Plan of Merger, by and among the Registrant, EPIX Delaware, Inc., a wholly-owned
  subsidiary of the Registrant, and Predix Pharmaceuticals Holdings, Inc. The maximum number of
  shares which may be sold upon the exercise of options issued under the plans or the issuance
  of stock awards granted under the 2003 Plan are subject to adjustment in accordance with
  certain anti-dilution and other provisions of the plans. Accordingly, pursuant to Rule&nbsp;416
  under the Securities Act of 1933, as amended (the &#147;Securities Act&#148;), this Registration
  Statement covers, in addition to the number of shares stated above, an indeterminate number of
  shares which may be subject to grant or otherwise issuable after the operation of any such
  anti-dilution and other provisions.</TD>
  </TR>
  
  <TR style="font-size: 3pt"><TD>&nbsp;</TD></TR>
  
  <TR valign="top">
      <TD nowrap align="left">(2)</TD>
      <TD>&nbsp;</TD>
      <TD>This calculation is made solely for the purpose of determining the registration fee pursuant
  to the provisions of Rule 457(c) and (h)&nbsp;under the Securities Act as follows: (i)&nbsp;in the case
  of shares of Common Stock which may be purchased upon exercise of outstanding options, the fee
  is calculated on the basis of the price at which the options may be exercised; and (ii)&nbsp;in the
  case of shares of Common Stock for which options have not yet been granted and/or stock awards
  have not yet been issued and the price of which is therefore unknown, the fee is calculated on
  the basis of the average of the high and low sale prices per share of the Common Stock on the
  NASDAQ Global Market as of a date (November 13, 2006) within five business days prior to
  filing this Registration Statement.</TD>
  </TR>
  
  </TABLE>
  
  
  
  <DIV style="width: 100%; border-bottom: 1pt solid black; margin-top: 10pt; font-size: 1pt">&nbsp;</DIV>
  <DIV style="width: 100%; border-bottom: 2pt solid black; font-size: 1pt">&nbsp;</DIV>
  
  
  
  
  
  <P align="center" style="font-size: 10pt"><!-- Folio -->&nbsp;<!-- /Folio -->
  </DIV>
  
  <!-- PAGEBREAK -->
  <P><HR noshade><P>
  <H5 align="left" style="page-break-before:always"><A HREF="#toc">Table of Contents</A></H5><P>
  
  <DIV style="font-family: 'Times New Roman',Times,serif">
  
  <DIV align="center" style="font-size: 10pt; margin-top: 18pt"><U>EXPLANATORY NOTE</U>
  </DIV>
  
  
  <DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Pursuant to a certain Agreement and Plan of Merger, dated as of April&nbsp;3, 2006, as amended, by
  and among the Registrant, a wholly owned subsidiary of the Registrant, EPIX Delaware, Inc., and
  Predix Pharmaceuticals Holdings, Inc. (&#147;Predix&#148;), on August&nbsp;16, 2006, the Registrant assumed all
  options to purchase Predix common stock then outstanding granted under the Predix Pharmaceuticals
  Holdings, Inc. Amended and Restated 2003 Stock Incentive Plan (the &#147;2003 Plan&#148;) and the Physiome
  Sciences, Inc. 1997 Stock Option Plan, as amended (the &#147;1997 Plan&#148;). In conjunction with its
  assumption of those options and the 2003 Plan and the 1997 Plan, the Registrant is registering on
  this Registration Statement an aggregate of 2,889,595 shares under the 2003 Plan and an aggregate
  of 3,710 shares under the 1997 Plan.
  </DIV>
  
  
  
  <P align="center" style="font-size: 10pt"><!-- Folio -->&nbsp;<!-- /Folio -->
  </DIV>
  
  <!-- PAGEBREAK -->
  <P><HR noshade><P>
  
  <DIV style="font-family: 'Times New Roman',Times,serif">
  
  
  
  
  <!-- TOC -->
  <A name="toc"><DIV align="CENTER" style="page-break-before:always"><U><B>TABLE OF CONTENTS</B></U></DIV></A>
  
  <P><CENTER>
  <TABLE border="0" width="90%" cellpadding="0" cellspacing="0">
  <TR>
  	<TD width="3%"></TD>
  	<TD width="3%"></TD>
  	<TD width="3%"></TD>
  	<TD width="3%"></TD>
  	<TD width="3%"></TD>
  	<TD width="3%"></TD>
  	<TD width="3%"></TD>
  	<TD width="3%"></TD>
  	<TD width="76%"></TD>
  </TR>
  <TR><TD colspan="9"><A HREF="#000">PART II</A></TD></TR>
  <TR><TD></TD><TD colspan="8"><A HREF="#001">Item&nbsp;3. Incorporation of Certain Documents by Reference</A></TD></TR>
  <TR><TD></TD><TD colspan="8"><A HREF="#002">Item&nbsp;4. Description of Securities</A></TD></TR>
  <TR><TD></TD><TD colspan="8"><A HREF="#003">Item&nbsp;5. Interests of Named Experts and Counsel</A></TD></TR>
  <TR><TD></TD><TD colspan="8"><A HREF="#004">Item&nbsp;6. Indemnification of Directors and Officers</A></TD></TR>
  <TR><TD></TD><TD colspan="8"><A HREF="#005">Item&nbsp;7. Exemption from Registration Claimed</A></TD></TR>
  <TR><TD></TD><TD colspan="8"><A HREF="#006">Item&nbsp;8. Exhibits</A></TD></TR>
  <TR><TD></TD><TD colspan="8"><A HREF="#007">Item&nbsp;9. Undertakings</A></TD></TR>
  <TR><TD colspan="9"><A HREF="#008">SIGNATURES</A></TD></TR>
  <TR><TD colspan="9"><A HREF="#009">EXHIBIT INDEX</A></TD></TR>
  <TR><TD colspan="9"><A HREF="b62534epexv5w1.htm">EX-5.1 Opinion of Goodwin Procter LLP</A></TD></TR>
  <TR><TD colspan="9"><A HREF="b62534epexv23w2.htm">EX-23.2 Consent of Ernst & Young LLP</A></TD></TR>
  </TABLE>
  </CENTER>
  <!-- /TOC -->
  <P><HR noshade><P>
  <H5 align="left" style="page-break-before:always"><A HREF="#toc">Table of Contents</A></H5><P>
  
  
  
  
  <!-- link1 "PART II" -->
  <DIV align="left"><A NAME="000"></A></DIV>
  
  <DIV align="center" style="font-size: 10pt; margin-top: 18pt"><B>PART II</B>
  </DIV>
  
  
  <DIV align="center" style="font-size: 10pt; margin-top: 6pt"><B>INFORMATION REQUIRED IN THE REGISTRATION STATEMENT</B>
  </DIV>
  
  <!-- link2 "Item&nbsp;3. Incorporation of Certain Documents by Reference" -->
  <DIV align="left"><A NAME="001"></A></DIV>
  
  <DIV align="left" style="font-size: 10pt; margin-top: 12pt"><U>Item&nbsp;3. Incorporation of Certain Documents by Reference</U>.
  </DIV>
  
  
  <DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The following documents filed by the Registrant with the Securities and Exchange Commission
  (the &#147;Commission&#148;) are incorporated herein by reference:
  </DIV>
  
  
  <DIV style="margin-top: 6pt">
  <TABLE width="100%" border="0" cellpadding="0" cellspacing="0" style="font-size: 10pt">
  
  <TR valign="top" style="font-size: 10pt; color: #000000; background: transparent">
      <TD width="2%" style="background: transparent">&nbsp;</TD>
      <TD width="2%" nowrap align="left">(a)</TD>
      <TD width="1%">&nbsp;</TD>
      <TD>The Registrant&#146;s Annual Report on Form 10-K for the fiscal year ended December&nbsp;31,
  2005, as filed on March&nbsp;1, 2006 and amended on April&nbsp;28, 2006.</TD>
  </TR>
  
  <TR>
      <TD style="font-size: 6pt">&nbsp;</TD>
  </TR><TR valign="top" style="font-size: 10pt; color: #000000; background: transparent">
      <TD width="2%" style="background: transparent">&nbsp;</TD>
      <TD width="2%" nowrap align="left">(b)</TD>
      <TD width="1%">&nbsp;</TD>
      <TD>The Registrant&#146;s Quarterly Reports on Form 10-Q for the quarters ended March&nbsp;31, 2006,
  June&nbsp;30, 2006 and September&nbsp;30, 2006.</TD>
  </TR>
  
  <TR>
      <TD style="font-size: 6pt">&nbsp;</TD>
  </TR><TR valign="top" style="font-size: 10pt; color: #000000; background: transparent">
      <TD width="2%" style="background: transparent">&nbsp;</TD>
      <TD width="2%" nowrap align="left">(c)</TD>
      <TD width="1%">&nbsp;</TD>
      <TD>The Registrant&#146;s Current Reports on Form 8-K, filed with the Commission on January&nbsp;10,
  2006, February&nbsp;1, 2006, February&nbsp;16, 2006, March&nbsp;9, 2006, April&nbsp;3, 2006, April&nbsp;26, 2006,
  May&nbsp;8, 2006, May&nbsp;24, 2006, July&nbsp;5, 2006, July&nbsp;12, 2006, July&nbsp;13, 2006, July&nbsp;20, 2006, July
  26, 2006, July&nbsp;28, 2006, July&nbsp;31, 2006, August&nbsp;15, 2006, August&nbsp;17, 2006 (as amended on
  August&nbsp;18, 2006 and October&nbsp;27, 2006), September&nbsp;7, 2006, September&nbsp;21, 2006, September&nbsp;22,
  2006, October&nbsp;23, 2006 and October&nbsp;26, 2006.</TD>
  </TR>
  
  <TR>
      <TD style="font-size: 6pt">&nbsp;</TD>
  </TR><TR valign="top" style="font-size: 10pt; color: #000000; background: transparent">
      <TD width="2%" style="background: transparent">&nbsp;</TD>
      <TD width="2%" nowrap align="left">(d)</TD>
      <TD width="1%">&nbsp;</TD>
      <TD>The Registrant&#146;s joint proxy statement/prospectus filed pursuant to Rule&nbsp;424(b)(3) of
  the Securities Act of 1933, as amended, with the SEC on July&nbsp;18, 2006 (Reg. No.
  333-133513).</TD>
  </TR>
  
  <TR>
      <TD style="font-size: 6pt">&nbsp;</TD>
  </TR><TR valign="top" style="font-size: 10pt; color: #000000; background: transparent">
      <TD width="2%" style="background: transparent">&nbsp;</TD>
      <TD width="2%" nowrap align="left">(e)</TD>
      <TD width="1%">&nbsp;</TD>
      <TD>The description of the Registrant&#146;s common stock contained in &#147;Description of Capital
  Stock&#148; in the registration statement on Form S-4 filed with the SEC on April&nbsp;25, 2006 (File
  No.&nbsp;333-33513) and any amendments or reports filed to update such description.</TD>
  </TR>
  
  </TABLE>
  </DIV>
  
  <DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;All reports and other documents filed by the Registrant after the date hereof pursuant to
  Sections&nbsp;13(a), 13(c), 14 and 15(d) of the Exchange Act prior to the filing of a post-effective
  amendment which indicates that all securities offered hereby have been sold or which deregisters
  all securities then remaining unsold, shall be deemed to be incorporated by reference herein and to
  be part hereof from the date of filing of such reports and documents.
  </DIV>
  
  <!-- link2 "Item&nbsp;4. Description of Securities" -->
  <DIV align="left"><A NAME="002"></A></DIV>
  
  <DIV align="left" style="font-size: 10pt; margin-top: 12pt"><U>Item&nbsp;4. Description of Securities</U>.
  </DIV>
  
  
  <DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Not applicable.
  </DIV>
  
  <!-- link2 "Item&nbsp;5. Interests of Named Experts and Counsel" -->
  <DIV align="left"><A NAME="003"></A></DIV>
  
  <DIV align="left" style="font-size: 10pt; margin-top: 12pt"><U>Item&nbsp;5. Interests of Named Experts and Counsel</U>.
  </DIV>
  
  
  <DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The validity of the issuance of the shares of common stock registered under this Registration
  Statement has been passed upon for the Registrant by Goodwin Procter LLP, Boston,
  Massachusetts.
  </DIV>
  
  <!-- link2 "Item&nbsp;6. Indemnification of Directors and Officers" -->
  <DIV align="left"><A NAME="004"></A></DIV>
  
  <DIV align="left" style="font-size: 10pt; margin-top: 12pt"><U>Item&nbsp;6. Indemnification of Directors and Officers</U>.
  </DIV>
  
  
  <DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The Registrant&#146;s Restated Certificate of Incorporation, as amended (the &#147;Restated
  Certificate&#148;) provides that the Registrant shall indemnify to the fullest extent authorized by the
  Delaware General Corporation Law (&#147;DGCL&#148;), each person who is involved in any litigation or other
  proceeding because such person is or was a director or officer of the Registrant or is or was
  serving as an officer or director of another entity at the request of the Registrant, against
  expenses (including attorneys&#146; fees), judgments, fines and amounts reasonably incurred in
  connection therewith. The Restated Certificate provides that the right to indemnification includes
  the right to be paid expenses incurred in defending any proceeding in advance of its final
  disposition; provided, however, that such advance payment will only be made upon delivery to the
  Registrant of an undertaking, by the director or officer, to repay all amounts so advanced if it is
  ultimately determined that such director or officer is not entitled to indemnification.
  </DIV>
  
  
  <P align="center" style="font-size: 10pt"><!-- Folio -->1<!-- /Folio -->
  </DIV>
  
  <!-- PAGEBREAK -->
  <P><HR noshade><P>
  <H5 align="left" style="page-break-before:always"><A HREF="#toc">Table of Contents</A></H5><P>
  
  <DIV style="font-family: 'Times New Roman',Times,serif">
  
  
  
  
  <DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Section&nbsp;145 of the DGCL permits a corporation to indemnify any director or officer of the
  corporation against expenses (including attorneys&#146; fees), judgments, fines and amounts paid in
  settlement actually and reasonably incurred in connection with any action, suit or proceeding
  brought by reason of the fact that such person is or was a director or officer of the corporation,
  if such person acted in good faith and in a manner that he or she reasonably believed to be in, or
  not opposed to, the best interests of the corporation, and, with respect to any criminal action or
  proceeding, if he or she had no reason to believe his or her conduct was unlawful. In a derivative
  action, (i.e., one brought by or on behalf of the corporation), indemnification may be made only
  for expenses, actually and reasonably incurred by any director or officer in connection with the
  defense or settlement of such an action or suit, if such person acted in good faith and in a manner
  that he reasonably believed to be in, or not opposed to, the best interests of the corporation,
  except that no indemnification shall be made if such person shall have been adjudged to be liable
  to the corporation, unless and only to the extent that the court in which the action or suit was
  brought shall determine that the defendant is fairly and reasonably entitled to indemnity for such
  expenses despite such adjudication of liability.
  </DIV>
  
  
  <DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Pursuant to Section&nbsp;102(b)(7) of the DGCL, the Restated Certificate eliminates the liability
  of a director or the corporation or its stockholders for monetary damages for such breach of
  fiduciary duty as a director, except for liabilities arising (i)&nbsp;from any breach of the director&#146;s
  duty of loyalty to the corporation or its stockholders, (ii)&nbsp;from acts or omissions not in good
  faith or which involve intentional misconduct or a knowing violation of law, (iii)&nbsp;under Section
  174 of the DGCL, or (iv)&nbsp;from any transaction from which the director derived an improper personal
  benefit. The Registrant has obtained insurance policies insuring the directors and officers of the
  Registrant against certain liabilities that they may incur in their capacity as directors and
  officers.
  </DIV>
  
  
  <DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The Registrant has entered into indemnification agreements (the &#147;Indemnification Agreements&#148;),
  with certain of its directors and certain of its officers. The Indemnification Agreements provide
  that the Registrant will, to the fullest extent permitted by law, pay any attorneys&#146; fees and all
  other costs, expenses and obligations paid or incurred by the indemnitee in connection with claims
  against him or her related to the fact that he or she was a director or officer of the Registrant
  or serving at the request of the Registrant in such capacity with another corporation, partnership,
  joint venture, employee benefit plan, trust or other enterprise. The payments to be made under the
  Indemnification Agreements include expenses, judgments, fines, penalties and amounts paid in
  settlement (including all interest, assessments and other judgments, fines, penalties or amounts
  paid in settlement) of such claims. If requested by the indemnitee, the Registrant shall advance
  all expenses to the indemnitee. Any payments made by the Registrant under the Indemnification
  Agreements are subrogated to all of the rights of recovery of the indemnitee. The rights of the
  indmenitee are in addition to such rights the indemnitee may have under the Registrant&#146;s Restated
  Certificate, the Registrant&#146;s by-laws and the DGCL.
  </DIV>
  
  
  <DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Pursuant to the Agreement and Plan of Merger by and among the Registrant, EPIX Delaware Inc.,
  a wholly-owned subsidiary of the Registrant, and Predix Pharmaceuticals Holdings, Inc. (&#147;Predix&#148;)
  dated as of April&nbsp;3, 2006, as amended, the Registrant agreed to fulfill and honor the obligations
  of Predix which existed prior to the merger to indemnify Predix&#146;s present and former directors and
  officers. The certificate of incorporation and by-laws of EPIX Delaware Inc. provide for the
  indemnification and elimination of liability for monetary damages to the same extent as set forth
  in Predix&#146;s certificate of incorporation and by-laws and such provision may not be amended,
  repealed or otherwise modified for a period of six years after the merger in any manner that would
  adversely affect the rights of the directors or officers of Predix at the time of the completion of
  the merger. The Registrant has agreed to guarantee the timely payment of all funds owing by, and
  the timely performance of all obligations of the EPIX Delaware, Inc. relating to these
  indemnification obligations.
  </DIV>
  
  <!-- link2 "Item&nbsp;7. Exemption from Registration Claimed" -->
  <DIV align="left"><A NAME="005"></A></DIV>
  
  <DIV align="left" style="font-size: 10pt; margin-top: 12pt"><U>Item&nbsp;7. Exemption from Registration Claimed</U>.
  </DIV>
  
  
  <DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Not applicable.
  </DIV>
  
  
  <P align="center" style="font-size: 10pt"><!-- Folio -->2<!-- /Folio -->
  </DIV>
  
  <!-- PAGEBREAK -->
  <P><HR noshade><P>
  <H5 align="left" style="page-break-before:always"><A HREF="#toc">Table of Contents</A></H5><P>
  
  
  <DIV style="font-family: 'Times New Roman',Times,serif">
  
  
  
  <!-- link2 "Item&nbsp;8. Exhibits" -->
  <DIV align="left"><A NAME="006"></A></DIV>
  
  <DIV align="left" style="font-size: 10pt; margin-top: 12pt"><U>Item&nbsp;8. Exhibits</U>.
  </DIV>
  
  <DIV align="center">
  <TABLE style="font-size: 10pt" cellspacing="0" border="0" cellpadding="0" width="100%">
  <!-- Begin Table Head -->
  <TR valign="bottom">
      <TD width="8%">&nbsp;</TD>
      <TD width="2%">&nbsp;</TD>
      <TD width="90%">&nbsp;</TD>
  </TR>
  <TR style="font-size: 8pt" valign="bottom">
      <TD nowrap align="left"><B>Exhibit</B></TD>
      <TD>&nbsp;</TD>
      <TD nowrap align="center">&nbsp;</TD>
  </TR>
  <TR style="font-size: 8pt" valign="bottom">
      <TD nowrap align="left"><B>Number</B></TD>
      <TD>&nbsp;</TD>
      <TD nowrap align="center"><B>Description</B></TD>
  </TR>
  
  <!-- End Table Head -->
  <!-- Begin Table Body -->
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:8px; text-indent:-0px">4.1
  </DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">Specimen certificate for shares of Common Stock of EPIX Pharmaceuticals, Inc. (filed
  as Exhibit&nbsp;4.1 to EPIX Pharmaceuticals Inc.&#146;s Quarterly Report on Form&nbsp;10-Q dated
  November&nbsp;9, 2006 and incorporated herein by reference).</TD>
  </TR>
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
  </TR>
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:8px; text-indent:-0px">5.1
  </DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">Opinion of Goodwin Procter LLP as to the legality of shares being registered.</TD>
  </TR>
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
  </TR>
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:8px; text-indent:-0px">23.1
  </DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">Consent of Goodwin Procter LLP (included in opinion of counsel filed as
  Exhibit&nbsp;5.1).</TD>
  </TR>
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
  </TR>
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:8px; text-indent:-0px">23.2
  </DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">Consent of Ernst &#038; Young LLP.</TD>
  </TR>
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
  </TR>
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:8px; text-indent:-0px">24.1
  </DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">Power of Attorney to file future amendments (set forth on the signature page of this
  Registration Statement).</TD>
  </TR>
  <!-- End Table Body -->
  </TABLE>
  </DIV>
  
  <!-- link2 "Item&nbsp;9. Undertakings" -->
  <DIV align="left"><A NAME="007"></A></DIV>
  
  <DIV align="left" style="font-size: 10pt; margin-top: 12pt"><U>Item&nbsp;9. Undertakings</U>.
  </DIV>
  
  
  <DIV style="margin-top: 6pt">
  <TABLE width="100%" border="0" cellpadding="0" cellspacing="0" style="font-size: 10pt">
  
  <TR valign="top" style="font-size: 10pt; color: #000000; background: transparent">
      <TD width="1%" nowrap align="left">(a)</TD>
      <TD width="1%">&nbsp;</TD>
      <TD>The undersigned Registrant hereby undertakes:</TD>
  </TR>
  
  <TR>
      <TD style="font-size: 6pt">&nbsp;</TD>
  </TR><TR valign="top" style="font-size: 10pt; color: #000000; background: transparent">
      <TD width="1%" nowrap align="left">(1)</TD>
      <TD width="1%">&nbsp;</TD>
      <TD>To file, during any period in which offers or sales are being made, a post-effective
  amendment to this registration statement:</TD>
  </TR>
  
  </TABLE>
  </DIV>
  
  
  <DIV align="left" style="font-size: 10pt; margin-top: 6pt; margin-left: 4%">(i)&nbsp;To include any prospectus required by Section&nbsp;10(a)(3) of the Securities Act of
  1933;
  </DIV>
  
  
  <DIV align="left" style="font-size: 10pt; margin-top: 6pt; margin-left: 4%">(ii)&nbsp;To reflect in the prospectus any facts or events arising after the effective
  date of the registration statement (or the most recent post-effective amendment
  thereof) which, individually or in the aggregate, represent a fundamental change in
  the information set forth in the registration statement. Notwithstanding the
  foregoing, any increase or decrease in volume of securities offered (if the total
  dollar value of securities offered would not exceed that which was registered) and
  any deviation from the low or high end of the estimated maximum offering range may
  be reflected in the form of prospectus filed with the Commission pursuant to Rule
  424(b) (&#167; 230.424(b) of this chapter) if, in the aggregate, the changes in volume
  and price represent no more than a 20% change in the maximum aggregate offering
  price set forth in the &#147;Calculation of Registration Fee&#148; table in the effective
  registration statement.
  </DIV>
  
  
  <DIV align="left" style="font-size: 10pt; margin-top: 6pt; margin-left: 4%">(iii)&nbsp;To include any material information with respect to the plan of distribution
  not previously disclosed in the registration statement or any material change to
  such information in the registration statement;
  </DIV>
  
  
  <DIV align="left" style="font-size: 10pt; margin-top: 6pt; margin-left: 4%"><I>Provided, however</I>, That:
  </DIV>
  
  <DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(A)&nbsp;Paragraphs (a)(1)(i) and (a)(1)(ii) of this section do not apply if the
  registration statement is on Form S-8 (&#167; 230.16b of this chapter), and the information
  required to be included in a post-effective amendment by those paragraphs is contained in
  reports filed with or furnished to the Commission by the Registrant pursuant to Section&nbsp;13
  or Section 15(d) of the Securities Exchange Act of 1934 (15 U.S.C. 78m or 78o(d)) that are
  incorporated by reference in this registration statement; and
  </DIV>
  
  
  <DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(B)&nbsp;Paragraphs (a)(1)(i), (a)(1)(ii) and (a)(1)(iii) of this section do not apply if
  the registration statement is on Form S-3 (&#167; 239.13 of this chapter) or Form F-3 (&#167; 239.33
  of this chapter) and the information required to be included in a post-effective amendment
  by those paragraphs is contained in reports filed with or furnished to the Commission by the
  Registrant pursuant to Section&nbsp;13 or Section 15(d) of the Securities Exchange Act of 1934
  that are incorporated by reference in the registration statement, or is contained in a form
  of prospectus filed pursuant to Rule 424(b) (&#167; 230.424(b) of this chapter) that is part of
  the registration statement.
  </DIV>
  
  
  <DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(C) <I>Provided further, however</I>, that paragraphs (a)(1)(i) and (a)(1)(ii) do not apply if
  the registration statement is for an offering of asset-backed securities on Form S-1 (&#167;
  239.11 of this chapter) or Form S-3 (&#167; 239.13 of this chapter), and the information required
  to be included in a post-effective amendment is provided pursuant to Item 1100(c) of
  Regulation&nbsp;AB (&#167; 229.1100(c)).
  </DIV>
  
  
  <P align="center" style="font-size: 10pt"><!-- Folio -->3<!-- /Folio -->
  </DIV>
  
  <!-- PAGEBREAK -->
  <P><HR noshade><P>
  <H5 align="left" style="page-break-before:always"><A HREF="#toc">Table of Contents</A></H5><P>
  
  <DIV style="font-family: 'Times New Roman',Times,serif">
  
  
  
  
  
  <DIV align="left" style="font-size: 10pt; margin-top: 6pt; margin-left: 3%">(2)&nbsp;That, for the purpose of determining any liability under the Securities Act of 1933,
  each such post-effective amendment shall be deemed to be a new registration statement
  relating to the securities offered therein, and the offering of such securities at that time
  shall be deemed to be the initial bona fide offering thereof.
  </DIV>
  
  
  <DIV align="left" style="font-size: 10pt; margin-top: 6pt; margin-left: 3%">(3)&nbsp;To remove from registration by means of a post-effective amendment any of the
  securities being registered which remain unsold at the termination of the offering.
  </DIV>
  
  <DIV style="margin-top: 6pt">
  <TABLE width="100%" border="0" cellpadding="0" cellspacing="0" style="font-size: 10pt">
  
  <TR valign="top" style="font-size: 10pt; color: #000000; background: transparent">
      <TD width="1%" nowrap align="left">(b)</TD>
      <TD width="1%">&nbsp;</TD>
      <TD>The undersigned Registrant hereby undertakes that, for purposes of determining any liability
  under the Securities Act of 1933, each filing of the Registrant&#146;s annual report pursuant to
  Section 13(a) or Section 15(d) of the Securities Exchange Act of 1934 (and, where applicable,
  each filing of an employee benefit plan&#146;s annual report pursuant to Section 15(d) of the
  Securities Exchange Act of 1934) that is incorporated by reference in this registration
  statement shall be deemed to be a new registration statement relating to the securities
  offered therein, and the offering of such securities at that time shall be deemed to be the
  initial bona fide offering thereof.</TD>
  </TR>
  
  <TR>
      <TD style="font-size: 6pt">&nbsp;</TD>
  </TR><TR valign="top" style="font-size: 10pt; color: #000000; background: transparent">
      <TD width="1%" nowrap align="left">(c)</TD>
      <TD width="1%">&nbsp;</TD>
      <TD>Insofar as indemnification for liabilities arising under the Securities Act of 1933 may be
  permitted to directors, officers and controlling persons of the Registrant pursuant to the
  foregoing provisions, or otherwise, the Registrant has been advised that in the opinion of the
  Securities and Exchange Commission such indemnification is against public policy as expressed
  in the Act and is, therefore, unenforceable. In the event that a claim for indemnification
  against such liabilities (other than the payment by the Registrant of expenses incurred or
  paid by a director, officer or controlling person of the Registrant in the successful defense
  of any action, suit or proceeding) is asserted by such director, officer or controlling person
  in connection with the securities being registered, the Registrant will, unless in the opinion
  of its counsel the matter has been settled by controlling precedent, submit to a court of
  appropriate jurisdiction the question whether such indemnification by it is against public
  policy as expressed in the Act and will be governed by the final adjudication of such issue.</TD>
  </TR>
  
  </TABLE>
  </DIV>
  <P align="center" style="font-size: 10pt"><!-- Folio -->4<!-- /Folio -->
  </DIV>
  
  <!-- PAGEBREAK -->
  <P><HR noshade><P>
  <H5 align="left" style="page-break-before:always"><A HREF="#toc">Table of Contents</A></H5><P>
  
  <DIV style="font-family: 'Times New Roman',Times,serif">
  
  
  <DIV style="margin-top: 6pt"><TABLE width="100%" border="0" cellpadding="0" cellspacing="0" style="font-size: 10pt">
  
  
  
  </TABLE>
  </DIV>
  <!-- link1 "SIGNATURES" -->
  <DIV align="left"><A NAME="008"></A></DIV>
  
  <DIV align="center" style="font-size: 10pt; margin-top: 12pt"><B>SIGNATURES</B>
  </DIV>
  
  
  <DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Pursuant to the requirements of the Securities Act of 1933, the Registrant certifies that it
  has reasonable grounds to believe that it meets all of the requirements for filing on Form S-8 and
  has duly caused this Registration Statement to be signed on its behalf by the undersigned,
  thereunto duly authorized, in Lexington, Massachusetts on November&nbsp;14, 2006.
  </DIV>
  
  <DIV align="center">
  <TABLE style="font-size: 10pt" cellspacing="0" border="0" cellpadding="0" width="100%">
  <!-- Begin Table Head -->
  <TR valign="bottom">
      <TD width="58%">&nbsp;</TD>
      <TD width="1%">&nbsp;</TD>
      <TD width="1%">&nbsp;</TD>
      <TD width="1%">&nbsp;</TD>
      <TD width="33%">&nbsp;</TD>
      <TD width="1%">&nbsp;</TD>
      <TD width="5%">&nbsp;</TD>
  </TR>
  <!-- End Table Head -->
  <!-- Begin Table Body -->
  <TR valign="bottom">
      <TD valign="top">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD colspan="3" valign="top" align="left"><B>EPIX PHARMACEUTICALS, INC.</B></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
  </TR>
  <TR valign="bottom"><!-- Blank Space -->
      <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
  </TR>
  
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;
  </DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">By:
  </TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">/s/ Michael G. Kauffman, M.D., Ph.D.</TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
  </TR>
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;
  </DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top"><DIV style="font-size: 1pt; border-top: 1px solid #000000">&nbsp;</DIV>
  Michael G. Kauffman, M.D., Ph.D.
  </TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
  </TR>
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;
  </DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">Chief Executive Officer</TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
  </TR>
  <!-- End Table Body -->
  </TABLE>
  </DIV>
  
  
  <DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Each person whose signature appears below constitutes and appoints Michael G. Kauffman and
  Kimberlee C. Drapkin, and each of them singly, his or her true and lawful attorneys-in-fact and
  agents, with full power of substitution and resubstitution in each of them singly, for him or her
  and in his or her name, place and stead, and in any and all capacities, to sign any and all
  amendments (including post-effective amendments) to this Registration Statement on Form S-8 of EPIX
  Pharmaceuticals, Inc., and to file the same, with all exhibits thereto and other documents in
  connection therewith, with the Securities and Exchange Commission, granting to the
  attorneys-in-fact and agents, and each of them, full power and authority to do and perform each and
  every act and thing requisite or necessary to be done in or about the premises, as full to all
  intents and purposes as he or she might or could do in person, hereby ratifying and confirming all
  that the attorneys-in-fact and agents or any of each of them or their substitute may lawfully do or
  cause to be done by virtue hereof.
  </DIV>
  
  
  <DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Pursuant to the requirements of the Securities Act of 1933, this Registration Statement has
  been signed by the following persons in the capacities and on the dates indicated.
  </DIV>
  
  <DIV align="center">
  <TABLE style="font-size: 10pt" cellspacing="0" border="0" cellpadding="0" width="100%">
  <!-- Begin Table Head -->
  <TR valign="bottom">
      <TD width="34%">&nbsp;</TD>
      <TD width="4%">&nbsp;</TD>
      <TD width="1%">&nbsp;</TD>
      <TD width="4%">&nbsp;</TD>
      <TD width="33%">&nbsp;</TD>
      <TD width="4%">&nbsp;</TD>
      <TD width="20%">&nbsp;</TD>
  </TR>
  <TR style="font-size: 8pt" valign="bottom">
      <TD nowrap align="left" style="border-bottom: 1px solid #000000">Signature</TD>
      <TD>&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD nowrap align="left" style="border-bottom: 1px solid #000000">Title</TD>
      <TD>&nbsp;</TD>
      <TD nowrap align="left" style="border-bottom: 1px solid #000000">Date</TD>
  </TR>
  <TR valign="bottom"><!-- Blank Space -->
      <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
  </TR>
  
  
  <!-- End Table Head -->
  <!-- Begin Table Body -->
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">/s/ Michael G. Kauffman, M.D., Ph.D.
  </DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">Chief Executive Officer and Director
  </TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">November&nbsp;14, 2006</TD>
  </TR>
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px"><DIV style="font-size: 1pt; border-top: 1px solid #000000">&nbsp;</DIV>
  Michael G. Kauffman, M.D., Ph.D.
  </DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;
  </TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">(Principal Executive Officer)</TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
  </TR>
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
  </TR>
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">/s/ Kimberlee C. Drapkin
  </DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">Chief Financial Officer
  </TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">November&nbsp;14, 2006</TD>
  </TR>
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px"><DIV style="font-size: 1pt; border-top: 1px solid #000000">&nbsp;</DIV>
  Kimberlee C. Drapkin
  </DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;
  </TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">(Principal Financial Officer and</TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
  </TR>
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;
  </DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">Principal Accounting Officer)</TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
  </TR>
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
  </TR>
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">/s/ Christopher F.O. Gabrieli
  </DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">Chairman of the Board
  </TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">November&nbsp;14, 2006</TD>
  </TR>
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px"><DIV style="font-size: 1pt; border-top: 1px solid #000000">&nbsp;</DIV>
  Christopher F.O. Gabrieli
  </DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
  </TR>
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
  </TR>
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">/s/ Patrick J. Fortune
  </DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">Director
  </TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">November&nbsp;14, 2006</TD>
  </TR>
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px"><DIV style="font-size: 1pt; border-top: 1px solid #000000">&nbsp;</DIV>
  Patrick J. Fortune
  </DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
  </TR>
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
  </TR>
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">/s/ Frederick Frank
  </DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">Director
  </TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">November&nbsp;14, 2006</TD>
  </TR>
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px"><DIV style="font-size: 1pt; border-top: 1px solid #000000">&nbsp;</DIV>
  Frederick Frank
  </DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
  </TR>
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
  </TR>
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">/s/ Michael Gilman
  </DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">Director
  </TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">November&nbsp;14, 2006</TD>
  </TR>
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px"><DIV style="font-size: 1pt; border-top: 1px solid #000000">&nbsp;</DIV>
  Michael Gilman
  </DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
  </TR>
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
  </TR>
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">/s/ Mark Leuchtenberger
  </DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">Director
  </TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">November&nbsp;14, 2006</TD>
  </TR>
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px"><DIV style="font-size: 1pt; border-top: 1px solid #000000">&nbsp;</DIV>
  Mark Leuchtenberger
  </DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
  </TR>
  <!-- End Table Body -->
  </TABLE>
  </DIV>
  
  
  <P align="center" style="font-size: 10pt"><!-- Folio -->5<!-- /Folio -->
  </DIV>
  
  <!-- PAGEBREAK -->
  <P><HR noshade><P>
  <H5 align="left" style="page-break-before:always"><A HREF="#toc">Table of Contents</A></H5><P>
  
  <DIV style="font-family: 'Times New Roman',Times,serif">
  
  <DIV align="center">
  <TABLE style="font-size: 10pt" cellspacing="0" border="0" cellpadding="0" width="100%">
  <!-- Begin Table Head -->
  <TR valign="bottom">
      <TD width="34%">&nbsp;</TD>
      <TD width="4%">&nbsp;</TD>
      <TD width="1%">&nbsp;</TD>
      <TD width="4%">&nbsp;</TD>
      <TD width="33%">&nbsp;</TD>
      <TD width="4%">&nbsp;</TD>
      <TD width="20%">&nbsp;</TD>
  </TR>
  <TR style="font-size: 8pt" valign="bottom">
      <TD nowrap align="left" style="border-bottom: 1px solid #000000">Signature</TD>
      <TD>&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD nowrap align="left" style="border-bottom: 1px solid #000000">Title</TD>
      <TD>&nbsp;</TD>
      <TD nowrap align="left" style="border-bottom: 1px solid #000000">Date</TD>
  </TR>
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
  </TR>
  
  <!-- End Table Head -->
  <!-- Begin Table Body -->
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">/s/ Robert J. Perez
  </DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">Director
  </TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">November&nbsp;14, 2006</TD>
  </TR>
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px"><DIV style="font-size: 1pt; border-top: 1px solid #000000">&nbsp;</DIV>
  Robert J. Perez
  </DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
  </TR>
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
  </TR>
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">/s/ Gregory D. Phelps
  </DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">Director
  </TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">November&nbsp;14, 2006</TD>
  </TR>
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px"><DIV style="font-size: 1pt; border-top: 1px solid #000000">&nbsp;</DIV>
  Gregory D. Phelps
  </DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
  </TR>
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
  </TR>
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">/s/ Ian F. Smith
  </DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">Director
  </TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">November&nbsp;14, 2006</TD>
  </TR>
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px"><DIV style="font-size: 1pt; border-top: 1px solid #000000">&nbsp;</DIV>
  Ian F. Smith
  </DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
  </TR>
  <!-- End Table Body -->
  </TABLE>
  </DIV>
  
  
  <P align="center" style="font-size: 10pt"><!-- Folio -->6<!-- /Folio -->
  </DIV>
  
  <!-- PAGEBREAK -->
  <P><HR noshade><P>
  <H5 align="left" style="page-break-before:always"><A HREF="#toc">Table of Contents</A></H5><P>
  
  <DIV style="font-family: 'Times New Roman',Times,serif">
  <!-- link1 "EXHIBIT INDEX" -->
  <DIV align="left"><A NAME="009"></A></DIV>
  
  <DIV align="center" style="font-size: 10pt; margin-top: 18pt"><B>EXHIBIT INDEX</B>
  </DIV>
  
  <DIV align="center">
  <TABLE style="font-size: 10pt" cellspacing="0" border="0" cellpadding="0" width="100%">
  <!-- Begin Table Head -->
  <TR valign="bottom">
      <TD width="8%">&nbsp;</TD>
      <TD width="2%">&nbsp;</TD>
      <TD width="90%">&nbsp;</TD>
  </TR>
  <TR style="font-size: 8pt" valign="bottom">
      <TD nowrap align="left"><B>Exhibit</B></TD>
      <TD>&nbsp;</TD>
      <TD nowrap align="center">&nbsp;</TD>
  </TR>
  <TR style="font-size: 8pt" valign="bottom">
      <TD nowrap align="left"><B>Number</B></TD>
      <TD>&nbsp;</TD>
      <TD nowrap align="center"><B>Description</B></TD>
  </TR>
  
  <!-- End Table Head -->
  <!-- Begin Table Body -->
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:8px; text-indent:-0px">4.1
  </DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">Specimen certificate for shares of Common Stock of EPIX Pharmaceuticals, Inc. (filed
  as Exhibit&nbsp;4.1 to EPIX Pharmaceuticals Inc.&#146;s Quarterly Report on Form&nbsp;10-Q dated
  November&nbsp;9, 2006 and incorporated herein by reference).</TD>
  </TR>
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
  </TR>
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:8px; text-indent:-0px">5.1
  </DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">Opinion of Goodwin Procter LLP as to the legality of shares being registered.</TD>
  </TR>
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
  </TR>
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:8px; text-indent:-0px">23.1
  </DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">Consent of Goodwin Procter LLP (included in opinion of counsel filed as
  Exhibit&nbsp;5.1).</TD>
  </TR>
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
  </TR>
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:8px; text-indent:-0px">23.2
  </DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">Consent of Ernst &#038; Young LLP.</TD>
  </TR>
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
  </TR>
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:8px; text-indent:-0px">24.1
  </DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">Power of Attorney to file future amendments (set forth on the signature page of this
  Registration Statement).</TD>
  </TR>
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  </DIV>
  
  
  
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text: sv8
  Table of Contents
  As filed with the Securities and Exchange Commission on November 14, 2006
  REGISTRATION NO. 333 -
  UNITED STATES SECURITIES AND EXCHANGE COMMISSION
  WASHINGTON, D.C. 20549
  FORM S-8
  REGISTRATION STATEMENT
  under the
  SECURITIES ACT OF 1933
  EPIX Pharmaceuticals, Inc.
  (
  Exact Name of Registrant as Specified in Its Charter)
  Delaware
  (
  State or Other Jurisdiction
  of Incorporation or Organization
  )
  04-3030815
  (
  I.R.S. Employer
  Identification No.
  )
  4 Maguire Road
  Lexington, Massachusetts 02421
  (
  Address, Including Zip Code, of Principal Executive Offices
  )
  PREDIX PHARMACEUTICALS HOLDINGS, INC.
  AMENDED AND RESTATED 2003 STOCK INCENTIVE PLAN
  PHYSIOME SCIENCES, INC. 1997 STOCK OPTION PLAN
  (Full Titles of the Plan)
  Michael G. Kauffman, M.D., Ph.D.
  Chief Executive Officer
  EPIX Pharmaceuticals, Inc.
  4 Maguire Road
  Lexington, Massachusetts 02421
  (781) 761-7600
  (
  Name, Address and Telephone Number, Including
  Area Code, of Agent For Service
  )
  with copies to:
  Edward A. King, Esq.
  Goodwin Procter LLP
  Exchange Place
  Boston, Massachusetts 02109
  (617) 570-1000
  CALCULATION OF REGISTRATION FEE
  Proposed
  Proposed
  Maximum
  Maximum
  Title of
  Amount to be
  Offering Price
  Aggregate
  Amount of
  Securities to be Registered
  Registered
  (1)
  Per Share
  (2)
  Offering Price
  Registration Fee
  Common Stock, $0.01 par value
  1,116,959 shares
  $
  4.21
  $
  4,702,397.39
  503.16
  Common Stock, $0.01 par value
  1,191,370 shares
  $
  0.98
  $
  1,167,542.60
  124.93
  Common Stock, $0.01 par value
  264,139 shares
  $
  1.74
  $
  459,601.86
  49.18
  Common Stock, $0.01 par value
  139,049 shares
  $
  2.18
  $
  303,126.82
  32.43
  Common Stock, $0.01 par value
  3,710 shares
  $
  2.28
  $
  8,458.80
  0.91
  Common Stock, $0.01 par value
  160,306 shares
  $
  3.62
  $
  580,307
  62.09
  Common Stock, $0.01 par value
  17,772 shares
  $
  6.53
  $
  116,051.16
  12.42
  Total
  2,893,305 shares
  N/A
  $
  7,337,486.35
  $
  785.11
  (1)
  The number of shares of common stock, par value $0.01 per share ("Common Stock"), stated
  above consists of the aggregate number of shares which may be sold upon (i) the exercise of
  options which have been granted or upon the exercise of options or issuance of stock awards
  which may hereafter be granted under the Predix Pharmaceuticals Holdings, Inc. Amended and
  Restated 2003 Stock Incentive Plan (the "2003 Plan"), and (ii) the exercise of options which
  have been granted under the Physiome Sciences, Inc. 1997 Stock Option Plan, as amended (the
  "1997 Plan") which plans were assumed by the Registrant on August 16, 2006, pursuant to an
  Agreement and Plan of Merger, by and among the Registrant, EPIX Delaware, Inc., a wholly-owned
  subsidiary of the Registrant, and Predix Pharmaceuticals Holdings, Inc. The maximum number of
  shares which may be sold upon the exercise of options issued under the plans or the issuance
  of stock awards granted under the 2003 Plan are subject to adjustment in accordance with
  certain anti-dilution and other provisions of the plans. Accordingly, pursuant to Rule 416
  under the Securities Act of 1933, as amended (the "Securities Act"), this Registration
  Statement covers, in addition to the number of shares stated above, an indeterminate number of
  shares which may be subject to grant or otherwise issuable after the operation of any such
  anti-dilution and other provisions.
  (2)
  This calculation is made solely for the purpose of determining the registration fee pursuant
  to the provisions of Rule 457(c) and (h) under the Securities Act as follows: (i) in the case
  of shares of Common Stock which may be purchased upon exercise of outstanding options, the fee
  is calculated on the basis of the price at which the options may be exercised; and (ii) in the
  case of shares of Common Stock for which options have not yet been granted and/or stock awards
  have not yet been issued and the price of which is therefore unknown, the fee is calculated on
  the basis of the average of the high and low sale prices per share of the Common Stock on the
  NASDAQ Global Market as of a date (November 13, 2006) within five business days prior to
  filing this Registration Statement.
  Table of Contents
  EXPLANATORY NOTE
  Pursuant to a certain Agreement and Plan of Merger, dated as of April 3, 2006, as amended, by
  and among the Registrant, a wholly owned subsidiary of the Registrant, EPIX Delaware, Inc., and
  Predix Pharmaceuticals Holdings, Inc. ("Predix"), on August 16, 2006, the Registrant assumed all
  options to purchase Predix common stock then outstanding granted under the Predix Pharmaceuticals
  Holdings, Inc. Amended and Restated 2003 Stock Incentive Plan (the "2003 Plan") and the Physiome
  Sciences, Inc. 1997 Stock Option Plan, as amended (the "1997 Plan"). In conjunction with its
  assumption of those options and the 2003 Plan and the 1997 Plan, the Registrant is registering on
  this Registration Statement an aggregate of 2,889,595 shares under the 2003 Plan and an aggregate
  of 3,710 shares under the 1997 Plan.
  TABLE OF CONTENTS
  PART II
  Item 3. Incorporation of Certain Documents by Reference
  Item 4. Description of Securities
  Item 5. Interests of Named Experts and Counsel
  Item 6. Indemnification of Directors and Officers
  Item 7. Exemption from Registration Claimed
  Item 8. Exhibits
  Item 9. Undertakings
  SIGNATURES
  EXHIBIT INDEX
  EX-5.1 Opinion of Goodwin Procter LLP
  EX-23.2 Consent of Ernst & Young LLP
  Table of Contents
  PART II
  INFORMATION REQUIRED IN THE REGISTRATION STATEMENT
  Item 3. Incorporation of Certain Documents by Reference
  .
  The following documents filed by the Registrant with the Securities and Exchange Commission
  (the "Commission") are incorporated herein by reference:
  (a)
  The Registrant's Annual Report on Form 10-K for the fiscal year ended December 31,
  2005, as filed on March 1, 2006 and amended on April 28, 2006.
  (b)
  The Registrant's Quarterly Reports on Form 10-Q for the quarters ended March 31, 2006,
  June 30, 2006 and September 30, 2006.
  (c)
  The Registrant's Current Reports on Form 8-K, filed with the Commission on January 10,
  2006, February 1, 2006, February 16, 2006, March 9, 2006, April 3, 2006, April 26, 2006,
  May 8, 2006, May 24, 2006, July 5, 2006, July 12, 2006, July 13, 2006, July 20, 2006, July
  26, 2006, July 28, 2006, July 31, 2006, August 15, 2006, August 17, 2006 (as amended on
  August 18, 2006 and October 27, 2006), September 7, 2006, September 21, 2006, September 22,
  2006, October 23, 2006 and October 26, 2006.
  (d)
  The Registrant's joint proxy statement/prospectus filed pursuant to Rule 424(b)(3) of
  the Securities Act of 1933, as amended, with the SEC on July 18, 2006 (Reg. No.
  333-133513).
  (e)
  The description of the Registrant's common stock contained in "Description of Capital
  Stock" in the registration statement on Form S-4 filed with the SEC on April 25, 2006 (File
  No. 333-33513) and any amendments or reports filed to update such description.
  All reports and other documents filed by the Registrant after the date hereof pursuant to
  Sections 13(a), 13(c), 14 and 15(d) of the Exchange Act prior to the filing of a post-effective
  amendment which indicates that all securities offered hereby have been sold or which deregisters
  all securities then remaining unsold, shall be deemed to be incorporated by reference herein and to
  be part hereof from the date of filing of such reports and documents.
  Item 4. Description of Securities
  .
  Not applicable.
  Item 5. Interests of Named Experts and Counsel
  .
  The validity of the issuance of the shares of common stock registered under this Registration
  Statement has been passed upon for the Registrant by Goodwin Procter LLP, Boston,
  Massachusetts.
  Item 6. Indemnification of Directors and Officers
  .
  The Registrant's Restated Certificate of Incorporation, as amended (the "Restated
  Certificate") provides that the Registrant shall indemnify to the fullest extent authorized by the
  Delaware General Corporation Law ("DGCL"), each person who is involved in any litigation or other
  proceeding because such person is or was a director or officer of the Registrant or is or was
  serving as an officer or director of another entity at the request of the Registrant, against
  expenses (including attorneys' fees), judgments, fines and amounts reasonably incurred in
  connection therewith. The Restated Certificate provides that the right to indemnification includes
  the right to be paid expenses incurred in defending any proceeding in advance of its final
  disposition; provided, however, that such advance payment will only be made upon delivery to the
  Registrant of an undertaking, by the director or officer, to repay all amounts so advanced if it is
  ultimately determined that such director or officer is not entitled to indemnification.
  1
  Table of Contents
  Section 145 of the DGCL permits a corporation to indemnify any director or officer of the
  corporation against expenses (including attorneys' fees), judgments, fines and amounts paid in
  settlement actually and reasonably incurred in connection with any action, suit or proceeding
  brought by reason of the fact that such person is or was a director or officer of the corporation,
  if such person acted in good faith and in a manner that he or she reasonably believed to be in, or
  not opposed to, the best interests of the corporation, and, with respect to any criminal action or
  proceeding, if he or she had no reason to believe his or her conduct was unlawful. In a derivative
  action, (i.e., one brought by or on behalf of the corporation), indemnification may be made only
  for expenses, actually and reasonably incurred by any director or officer in connection with the
  defense or settlement of such an action or suit, if such person acted in good faith and in a manner
  that he reasonably believed to be in, or not opposed to, the best interests of the corporation,
  except that no indemnification shall be made if such person shall have been adjudged to be liable
  to the corporation, unless and only to the extent that the court in which the action or suit was
  brought shall determine that the defendant is fairly and reasonably entitled to indemnity for such
  expenses despite such adjudication of liability.
  Pursuant to Section 102(b)(7) of the DGCL, the Restated Certificate eliminates the liability
  of a director or the corporation or its stockholders for monetary damages for such breach of
  fiduciary duty as a director, except for liabilities arising (i) from any breach of the director's
  duty of loyalty to the corporation or its stockholders, (ii) from acts or omissions not in good
  faith or which involve intentional misconduct or a knowing violation of law, (iii) under Section
  174 of the DGCL, or (iv) from any transaction from which the director derived an improper personal
  benefit. The Registrant has obtained insurance policies insuring the directors and officers of the
  Registrant against certain liabilities that they may incur in their capacity as directors and
  officers.
  The Registrant has entered into indemnification agreements (the "Indemnification Agreements"),
  with certain of its directors and certain of its officers. The Indemnification Agreements provide
  that the Registrant will, to the fullest extent permitted by law, pay any attorneys' fees and all
  other costs, expenses and obligations paid or incurred by the indemnitee in connection with claims
  against him or her related to the fact that he or she was a director or officer of the Registrant
  or serving at the request of the Registrant in such capacity with another corporation, partnership,
  joint venture, employee benefit plan, trust or other enterprise. The payments to be made under the
  Indemnification Agreements include expenses, judgments, fines, penalties and amounts paid in
  settlement (including all interest, assessments and other judgments, fines, penalties or amounts
  paid in settlement) of such claims. If requested by the indemnitee, the Registrant shall advance
  all expenses to the indemnitee. Any payments made by the Registrant under the Indemnification
  Agreements are subrogated to all of the rights of recovery of the indemnitee. The rights of the
  indmenitee are in addition to such rights the indemnitee may have under the Registrant's Restated
  Certificate, the Registrant's by-laws and the DGCL.
  Pursuant to the Agreement and Plan of Merger by and among the Registrant, EPIX Delaware Inc.,
  a wholly-owned subsidiary of the Registrant, and Predix Pharmaceuticals Holdings, Inc. ("Predix")
  dated as of April 3, 2006, as amended, the Registrant agreed to fulfill and honor the obligations
  of Predix which existed prior to the merger to indemnify Predix's present and former directors and
  officers. The certificate of incorporation and by-laws of EPIX Delaware Inc. provide for the
  indemnification and elimination of liability for monetary damages to the same extent as set forth
  in Predix's certificate of incorporation and by-laws and such provision may not be amended,
  repealed or otherwise modified for a period of six years after the merger in any manner that would
  adversely affect the rights of the directors or officers of Predix at the time of the completion of
  the merger. The Registrant has agreed to guarantee the timely payment of all funds owing by, and
  the timely performance of all obligations of the EPIX Delaware, Inc. relating to these
  indemnification obligations.
  Item 7. Exemption from Registration Claimed
  .
  Not applicable.
  2
  Table of Contents
  Item 8. Exhibits
  .
  Exhibit
  Number
  Description
  4.1
  Specimen certificate for shares of Common Stock of EPIX Pharmaceuticals, Inc. (filed
  as Exhibit 4.1 to EPIX Pharmaceuticals Inc.'s Quarterly Report on Form 10-Q dated
  November 9, 2006 and incorporated herein by reference).
  5.1
  Opinion of Goodwin Procter LLP as to the legality of shares being registered.
  23.1
  Consent of Goodwin Procter LLP (included in opinion of counsel filed as
  Exhibit 5.1).
  23.2
  Consent of Ernst & Young LLP.
  24.1
  Power of Attorney to file future amendments (set forth on the signature page of this
  Registration Statement).
  Item 9. Undertakings
  .
  (a)
  The undersigned Registrant hereby undertakes:
  (1)
  To file, during any period in which offers or sales are being made, a post-effective
  amendment to this registration statement:
  (i) To include any prospectus required by Section 10(a)(3) of the Securities Act of
  1933;
  (ii) To reflect in the prospectus any facts or events arising after the effective
  date of the registration statement (or the most recent post-effective amendment
  thereof) which, individually or in the aggregate, represent a fundamental change in
  the information set forth in the registration statement. Notwithstanding the
  foregoing, any increase or decrease in volume of securities offered (if the total
  dollar value of securities offered would not exceed that which was registered) and
  any deviation from the low or high end of the estimated maximum offering range may
  be reflected in the form of prospectus filed with the Commission pursuant to Rule
  424(b) (§ 230.424(b) of this chapter) if, in the aggregate, the changes in volume
  and price represent no more than a 20% change in the maximum aggregate offering
  price set forth in the "Calculation of Registration Fee" table in the effective
  registration statement.
  (iii) To include any material information with respect to the plan of distribution
  not previously disclosed in the registration statement or any material change to
  such information in the registration statement;
  Provided, however
  , That:
  (A) Paragraphs (a)(1)(i) and (a)(1)(ii) of this section do not apply if the
  registration statement is on Form S-8 (§ 230.16b of this chapter), and the information
  required to be included in a post-effective amendment by those paragraphs is contained in
  reports filed with or furnished to the Commission by the Registrant pursuant to Section 13
  or Section 15(d) of the Securities Exchange Act of 1934 (15 U.S.C. 78m or 78o(d)) that are
  incorporated by reference in this registration statement; and
  (B) Paragraphs (a)(1)(i), (a)(1)(ii) and (a)(1)(iii) of this section do not apply if
  the registration statement is on Form S-3 (§ 239.13 of this chapter) or Form F-3 (§ 239.33
  of this chapter) and the information required to be included in a post-effective amendment
  by those paragraphs is contained in reports filed with or furnished to the Commission by the
  Registrant pursuant to Section 13 or Section 15(d) of the Securities Exchange Act of 1934
  that are incorporated by reference in the registration statement, or is contained in a form
  of prospectus filed pursuant to Rule 424(b) (§ 230.424(b) of this chapter) that is part of
  the registration statement.
  (C)
  Provided further, however
  , that paragraphs (a)(1)(i) and (a)(1)(ii) do not apply if
  the registration statement is for an offering of asset-backed securities on Form S-1 (§
  239.11 of this chapter) or Form S-3 (§ 239.13 of this chapter), and the information required
  to be included in a post-effective amendment is provided pursuant to Item 1100(c) of
  Regulation AB (§ 229.1100(c)).
  3
  Table of Contents
  (2) That, for the purpose of determining any liability under the Securities Act of 1933,
  each such post-effective amendment shall be deemed to be a new registration statement
  relating to the securities offered therein, and the offering of such securities at that time
  shall be deemed to be the initial bona fide offering thereof.
  (3) To remove from registration by means of a post-effective amendment any of the
  securities being registered which remain unsold at the termination of the offering.
  (b)
  The undersigned Registrant hereby undertakes that, for purposes of determining any liability
  under the Securities Act of 1933, each filing of the Registrant's annual report pursuant to
  Section 13(a) or Section 15(d) of the Securities Exchange Act of 1934 (and, where applicable,
  each filing of an employee benefit plan's annual report pursuant to Section 15(d) of the
  Securities Exchange Act of 1934) that is incorporated by reference in this registration
  statement shall be deemed to be a new registration statement relating to the securities
  offered therein, and the offering of such securities at that time shall be deemed to be the
  initial bona fide offering thereof.
  (c)
  Insofar as indemnification for liabilities arising under the Securities Act of 1933 may be
  permitted to directors, officers and controlling persons of the Registrant pursuant to the
  foregoing provisions, or otherwise, the Registrant has been advised that in the opinion of the
  Securities and Exchange Commission such indemnification is against public policy as expressed
  in the Act and is, therefore, unenforceable. In the event that a claim for indemnification
  against such liabilities (other than the payment by the Registrant of expenses incurred or
  paid by a director, officer or controlling person of the Registrant in the successful defense
  of any action, suit or proceeding) is asserted by such director, officer or controlling person
  in connection with the securities being registered, the Registrant will, unless in the opinion
  of its counsel the matter has been settled by controlling precedent, submit to a court of
  appropriate jurisdiction the question whether such indemnification by it is against public
  policy as expressed in the Act and will be governed by the final adjudication of such issue.
  4
  Table of Contents
  SIGNATURES
  Pursuant to the requirements of the Securities Act of 1933, the Registrant certifies that it
  has reasonable grounds to believe that it meets all of the requirements for filing on Form S-8 and
  has duly caused this Registration Statement to be signed on its behalf by the undersigned,
  thereunto duly authorized, in Lexington, Massachusetts on November 14, 2006.
  EPIX PHARMACEUTICALS, INC.
  By:
  /s/ Michael G. Kauffman, M.D., Ph.D.
  Michael G. Kauffman, M.D., Ph.D.
  Chief Executive Officer
  Each person whose signature appears below constitutes and appoints Michael G. Kauffman and
  Kimberlee C. Drapkin, and each of them singly, his or her true and lawful attorneys-in-fact and
  agents, with full power of substitution and resubstitution in each of them singly, for him or her
  and in his or her name, place and stead, and in any and all capacities, to sign any and all
  amendments (including post-effective amendments) to this Registration Statement on Form S-8 of EPIX
  Pharmaceuticals, Inc., and to file the same, with all exhibits thereto and other documents in
  connection therewith, with the Securities and Exchange Commission, granting to the
  attorneys-in-fact and agents, and each of them, full power and authority to do and perform each and
  every act and thing requisite or necessary to be done in or about the premises, as full to all
  intents and purposes as he or she might or could do in person, hereby ratifying and confirming all
  that the attorneys-in-fact and agents or any of each of them or their substitute may lawfully do or
  cause to be done by virtue hereof.
  Pursuant to the requirements of the Securities Act of 1933, this Registration Statement has
  been signed by the following persons in the capacities and on the dates indicated.
  Signature
  Title
  Date
  /s/ Michael G. Kauffman, M.D., Ph.D.
  Chief Executive Officer and Director
  November 14, 2006
  Michael G. Kauffman, M.D., Ph.D.
  (Principal Executive Officer)
  /s/ Kimberlee C. Drapkin
  Chief Financial Officer
  November 14, 2006
  Kimberlee C. Drapkin
  (Principal Financial Officer and
  Principal Accounting Officer)
  /s/ Christopher F.O. Gabrieli
  Chairman of the Board
  November 14, 2006
  Christopher F.O. Gabrieli
  /s/ Patrick J. Fortune
  Director
  November 14, 2006
  Patrick J. Fortune
  /s/ Frederick Frank
  Director
  November 14, 2006
  Frederick Frank
  /s/ Michael Gilman
  Director
  November 14, 2006
  Michael Gilman
  /s/ Mark Leuchtenberger
  Director
  November 14, 2006
  Mark Leuchtenberger
  5
  Table of Contents
  Signature
  Title
  Date
  /s/ Robert J. Perez
  Director
  November 14, 2006
  Robert J. Perez
  /s/ Gregory D. Phelps
  Director
  November 14, 2006
  Gregory D. Phelps
  /s/ Ian F. Smith
  Director
  November 14, 2006
  Ian F. Smith
  6
  Table of Contents
  EXHIBIT INDEX
  Exhibit
  Number
  Description
  4.1
  Specimen certificate for shares of Common Stock of EPIX Pharmaceuticals, Inc. (filed
  as Exhibit 4.1 to EPIX Pharmaceuticals Inc.'s Quarterly Report on Form 10-Q dated
  November 9, 2006 and incorporated herein by reference).
  5.1
  Opinion of Goodwin Procter LLP as to the legality of shares being registered.
  23.1
  Consent of Goodwin Procter LLP (included in opinion of counsel filed as
  Exhibit 5.1).
  23.2
  Consent of Ernst & Young LLP.
  24.1
  Power of Attorney to file future amendments (set forth on the signature page of this
  Registration Statement).
  7