content: <HTML>
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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: 18pt">As filed with the Securities and Exchange Commission on September&nbsp;29, 2006
  </DIV>
  
  
  <DIV align="right" style="font-size: 10pt; margin-top: 12pt">Registration No.&nbsp;333-_____
  </DIV>
  
  
  <DIV style="width: 100%; border-bottom: 2pt solid black; font-size: 1pt">&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>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: 18pt; margin-top: 12pt"><B>FORM S-8</B>
  </DIV>
  
  
  <DIV align="center" style="font-size: 12pt; margin-top: 12pt"><B>REGISTRATION STATEMENT UNDER<BR>
  THE SECURITIES ACT OF 1933</B>
  </DIV>
  
  <DIV align="center" style="font-size: 24pt; margin-top: 12pt"><B>Idera Pharmaceuticals, Inc.</B>
  </DIV>
  
  <DIV align="center" style="font-size: 10pt">(Exact Name of Registrant as Specified in Its Charter)</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>
  (State or Other Jurisdiction of <BR>
  Incorporation or Organization)
  </TD>
      <TD>&nbsp;</TD>
      <TD align="center" valign="top"><B>04-3072298</B><BR>
  (I.R.S. Employer<BR>
  Identification No.)</TD>
  </TR>
  <TR valign="bottom"><!-- Blank Space -->
      <TD align="center" valign="top">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD align="center" valign="top">&nbsp;</TD>
  </TR>
  <TR valign="bottom">
      <TD align="center" valign="top"><B>345 Vassar Street <BR>
  Cambridge, Massachusetts</B><BR>
  (Address of Principal Executive Offices)
  </TD>
      <TD>&nbsp;</TD>
      <TD align="center" valign="top"><B>02139</B><BR>
  (Zip Code)</TD>
  </TR>
  <!-- End Table Body -->
  </TABLE>
  </DIV>
  
  
  <DIV align="center" style="font-size: 10pt; margin-top: 18pt"><B>2005 Stock Incentive Plan</B><BR>
  (Full Title of the Plan)
  </DIV>
  
  
  <DIV align="center" style="font-size: 10pt; margin-top: 18pt"><B>Sudhir Agrawal, D. Phil.<BR>
  Chief Executive Officer<BR>
  Idera Pharmaceuticals, Inc.<BR>
  345 Vassar Street<BR>
  Cambridge, Massachusetts 02139</B><BR>
  (Name and Address of Agent For Service)<BR>
  <B>(617)&nbsp;679-5500</B><BR>
  (Telephone Number, Including Area Code, of Agent For Service)
  </DIV>
  
  
  <DIV align="center" style="font-size: 10pt; margin-top: 18pt"><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">
      <TD width="41%">&nbsp;</TD>
      <TD width="3%">&nbsp;</TD>
      <TD width="1%">&nbsp;</TD>
      <TD width="11%">&nbsp;</TD>
      <TD width="1%">&nbsp;</TD>
      <TD width="5%">&nbsp;</TD>
      <TD width="1%">&nbsp;</TD>
      <TD width="5%">&nbsp;</TD>
      <TD width="1%">&nbsp;</TD>
      <TD width="5%">&nbsp;</TD>
      <TD width="1%">&nbsp;</TD>
      <TD width="12%">&nbsp;</TD>
      <TD width="1%">&nbsp;</TD>
      <TD width="5%">&nbsp;</TD>
      <TD width="1%">&nbsp;</TD>
      <TD width="5%">&nbsp;</TD>
      <TD width="1%">&nbsp;</TD>
  </TR>
  <TR style="font-size: 10pt" valign="bottom">
      <TD>&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD nowrap align="center" colspan="2">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD nowrap align="center" colspan="2">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD nowrap align="center" colspan="2">&nbsp;</TD>
      <TD>&nbsp;</TD>
  </TR>
  <TR style="font-size: 10pt" valign="bottom">
      <TD nowrap align="center">Title of Securities</TD>
      <TD>&nbsp;</TD>
      <TD nowrap align="center" colspan="2">Amount to be</TD>
      <TD>&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD nowrap align="center" colspan="2">Proposed<BR>Maximum<BR>Offering Price</TD>
      <TD>&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD nowrap align="center" colspan="2">Proposed<BR>Maximum<BR>Aggregate</TD>
      <TD>&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD nowrap align="center" colspan="2">Amount of<BR>Registration</TD>
      <TD>&nbsp;</TD>
  </TR>
  <TR style="font-size: 10pt" valign="bottom">
      <TD nowrap align="center" style="border-bottom: 1px solid #000000">to be Registered</TD>
      <TD>&nbsp;</TD>
      <TD nowrap align="center" colspan="2" style="border-bottom: 1px solid #000000">Registered(1)</TD>
      <TD>&nbsp;</TD>
      <TD>&nbsp;</TD>
  
  <TD nowrap align="center" colspan="2" style="border-bottom: 1px solid #000000">Per Share</TD>
      <TD>&nbsp;</TD>
      <TD>&nbsp;</TD>
  
  <TD nowrap align="center" colspan="2" style="border-bottom: 1px solid #000000">Offering Price</TD>
      <TD>&nbsp;</TD>
      <TD>&nbsp;</TD>
  
  <TD nowrap align="center" colspan="2" style="border-bottom: 1px solid #000000">Fee</TD>
      <TD>&nbsp;</TD>
  </TR>
  
  <!-- End Table Head -->
  <!-- Begin Table Body -->
  <TR valign="bottom">
      <TD><DIV style="margin-left:15px; text-indent:-15px">Common Stock,
  $0.001 par value
  per share
  (including the
  associated
  Preferred Stock
  Purchase Rights)</DIV></TD>
      <TD>&nbsp;</TD>
      <TD colspan="3" align="center">500,000 shares</TD>
      <TD>&nbsp;</TD>
      <TD nowrap align="left">&nbsp;</TD>
      <TD align="center">$3.43(2)</TD>
      <TD nowrap>&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD nowrap align="left">&nbsp;</TD>
      <TD align="center">$1,715,000(2)</TD>
      <TD nowrap>&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD align="left">&nbsp;</TD>
      <TD align="center">$183.51</TD>
      <TD>&nbsp;</TD>
  </TR>
  <!-- End Table Body -->
  </TABLE>
  </DIV>
  
  
  
  <P>
  <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>In accordance with Rule&nbsp;416 under the Securities Act of 1933, as amended, this
  registration statement shall be deemed to cover any additional securities that may from time
  to time be offered or issued to prevent dilution resulting from stock splits, stock dividends
  or similar transactions.</TD>
  </TR>
  
  <TR style="font-size: 3pt"><TD>&nbsp;</TD></TR>
  
  <TR valign="top">
      <TD nowrap align="left">(2)</TD>
      <TD>&nbsp;</TD>
      <TD>Estimated solely for the purpose of calculating the registration fee pursuant to Rules 457(c)
  and 457(h) of the Securities Act of 1933, as amended, and based upon the average of the high
  and low prices of the Registrant&#146;s common stock as reported on the American Stock Exchange on
  September&nbsp;26, 2006.</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>
  
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  <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">
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  	<TD width="3%"></TD>
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  	<TD width="3%"></TD>
  	<TD width="76%"></TD>
  </TR>
  <TR><TD colspan="9"><A HREF="#000">STATEMENT OF INCORPORATION BY REFERENCE</A></TD></TR>
  <TR><TD></TD><TD colspan="8"><A HREF="#001">Item&nbsp;5. Interests of Named Experts and Counsel.</A></TD></TR>
  <TR><TD></TD><TD colspan="8"><A HREF="#002">Item&nbsp;8. Exhibits.</A></TD></TR>
  <TR><TD colspan="9"><A HREF="#003">SIGNATURES</A></TD></TR>
  <TR><TD colspan="9"><A HREF="#004">INDEX TO EXHIBITS</A></TD></TR>
  <TR><TD colspan="9"><A HREF="b62525s8exv5w1.htm">EX-5.1 OPINION OF WILMER CUTLER PICKERING HALE AND DORR LLP</A></TD></TR>
  <TR><TD colspan="9"><A HREF="b62525s8exv23w1.htm">EX-23.1 CONSENT OF ERNST AND 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 "STATEMENT OF INCORPORATION BY REFERENCE" -->
  <DIV align="left"><A NAME="000"></A></DIV>
  
  <DIV align="center" style="font-size: 10pt; margin-top: 18pt"><B>STATEMENT OF INCORPORATION BY REFERENCE</B>
  </DIV>
  
  
  <DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;This Registration Statement on Form S-8 is filed to register the offer and sale of an
  additional 500,000 shares of the Registrant&#146;s common stock, $0.001 par value per share, to be
  issued under the Registrant&#146;s 2005 Stock Incentive Plan. This Registration Statement incorporates
  by reference the contents of the registration statement on form S-8, File No.&nbsp;333-126664, filed by
  the Registrant on July&nbsp;18, 2005, relating to the Registrant&#146;s 2005 Stock Incentive Plan.
  </DIV>
  <!-- link2 "Item&nbsp;5. Interests of Named Experts and Counsel." -->
  <DIV align="left"><A NAME="001"></A></DIV>
  
  <DIV align="left" style="font-size: 10pt; margin-top: 12pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<B>Item&nbsp;5. Interests of Named Experts and Counsel.</B>
  </DIV>
  
  
  <DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Wilmer Cutler Pickering Hale and Dorr LLP has opined as to the legality of the securities
  being offered by this registration statement.
  </DIV>
  <!-- link2 "Item&nbsp;8. Exhibits." -->
  <DIV align="left"><A NAME="002"></A></DIV>
  
  <DIV align="left" style="font-size: 10pt; margin-top: 12pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<B>Item&nbsp;8. Exhibits.</B>
  </DIV>
  
  
  <DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The Exhibit&nbsp;Index immediately preceding the exhibits is incorporated herein by reference.
  </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">
  <!-- link1 "SIGNATURES" -->
  <DIV align="left"><A NAME="003"></A></DIV>
  
  <DIV align="center" style="font-size: 10pt; margin-top: 18pt"><B>SIGNATURES</B>
  </DIV>
  
  
  <DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Pursuant to the requirements of the Securities Act of 1933, as amended, 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 Cambridge, Massachusetts, on September&nbsp;21,
  2006.
  </DIV>
  
  <TABLE width="100%" border="0" cellspacing="0" cellpadding="0" style="font-size: 10pt">
  <TR>
      <TD width="48%">&nbsp;</TD>
      <TD width="1%">&nbsp;</TD>
      <TD width="1%">&nbsp;</TD>
      <TD width="35%">&nbsp;</TD>
      <TD width="15%">&nbsp;</TD>
  </TR>
  <TR>
      <TD valign="top" align="left">&nbsp;</TD>
      <TD colspan="3" align="left">Idera Pharmaceuticals, Inc.<BR>
  &nbsp;</TD>
      <TD>&nbsp;</TD>
  </TR><TR>
      <TD align="left">&nbsp;</TD>
      <TD valign="top">By:&nbsp;&nbsp;</TD>
      <TD colspan="2" style="border-bottom: 1px solid #000000" align="left">/s/ Sudhir Agrawal
  &nbsp;</TD>
      <TD>&nbsp;</TD>
  </TR><TR>
      <TD align="left">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD colspan="2" align="left">Sudhir Agrawal, D. Phil.&nbsp;</TD>
      <TD>&nbsp;</TD>
  </TR><TR>
      <TD align="left">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD colspan="2" align="left">Chief Executive Officer&nbsp;</TD>
      <TD>&nbsp;</TD>
  </TR>
  <TR>
      <TD colspan="5">&nbsp;</TD>
  </TR>
  </TABLE>
  
  <DIV align="center" style="font-size: 10pt; margin-top: 18pt"><B>POWER OF ATTORNEY AND SIGNATURES</B>
  </DIV>
  
  
  
  <DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;We, the undersigned officers and directors of Idera Pharmaceuticals, Inc., hereby severally
  constitute and appoint Sudhir Agrawal, Robert W. Karr and Robert G. Andersen and each of
  them singly, our true and lawful attorneys with full power to them, and each of them singly, to
  sign for us and in our names in the capacities indicated below, the registration statement on Form
  S-8 filed herewith and any and all subsequent amendments to said registration statement, and
  generally to do all such things in our names and on our behalf in our capacities as officers and
  directors to enable Idera Pharmaceuticals, Inc. to comply with the provisions of the Securities Act
  of 1933, as amended, and all requirements of the Securities and Exchange Commission, hereby
  ratifying and confirming our signatures as they may be signed by our said attorneys, or any of
  them, to said registration statement and any and all amendments thereto.
  </DIV>
  
  <DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Pursuant to the requirements of the Securities Act of 1933, as amended, 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="30%">&nbsp;</TD>
      <TD width="5%">&nbsp;</TD>
      <TD width="30%">&nbsp;</TD>
      <TD width="5%">&nbsp;</TD>
      <TD width="30%">&nbsp;</TD>
  </TR>
  <TR style="font-size: 10pt" valign="bottom">
      <TD nowrap align="center"><U>Signature</U></TD>
      <TD>&nbsp;</TD>
      <TD nowrap align="center"><U>Title</U></TD>
      <TD>&nbsp;</TD>
      <TD nowrap align="center"><U>Date</U></TD>
  </TR>
  
  <!-- End Table Head -->
  <!-- Begin Table Body -->
  <TR valign="bottom"><!-- Blank Space -->
      <TD align="right">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD align="center" nowrap valign="top"><DIV style="margin-left:15px; text-indent:-15px">&nbsp;</DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
  </TR>
  <TR valign="bottom" style="padding-top: 1em">
      <TD align="left" nowrap valign="top">/s/  James B. Wyngaarden
  <DIV style="font-size: 1pt; border-top: 1px solid #000000">&nbsp;</DIV>
  James B. Wyngaarden, M.D.</TD>
      <TD>&nbsp;</TD>
      <TD align="left">
  Chairman of the Board of Directors<BR><BR>
  </TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">September 21, 2006</TD>
  </TR>
  <TR valign="bottom" style="padding-top: 1em">
      <TD align="left" nowrap valign="top">/s/ Sudhir Agrawal
  <DIV style="font-size: 1pt; border-bottom: 1px solid #000000">&nbsp;</DIV>
  Sudhir Agrawal, D. Phil</TD>
      <TD>&nbsp;</TD>
      <TD align="left">
  Chief Executive Officer, Chief
  Scientific Officer and Director
  (Principal Executive Officer)
  </TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">September 21, 2006</TD>
  </TR>
  <TR valign="bottom" style="padding-top: 1em">
      <TD align="left" nowrap valign="top">/s/ Robert W. Karr
  <DIV style="font-size: 1pt; border-bottom: 1px solid #000000">&nbsp;</DIV>
  Robert W. Karr, M.D.</TD>
      <TD>&nbsp;</TD>
      <TD align="left">
  President and Director<BR><BR>
  </TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">September 21, 2006</TD>
  </TR>
  <TR valign="bottom" style="padding-top: 1em">
      <TD align="left" nowrap valign="top">/s/  Robert G. Andersen
  <DIV style="font-size: 1pt; border-bottom: 1px solid #000000">&nbsp;</DIV>
  Robert G. Andersen</TD>
      <TD>&nbsp;</TD>
      <TD align="left">
  Chief Financial Officer, Vice
  President of Operations,
  Treasurer and Secretary
  (Principal Financial and
  Accounting Officer)
  </TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">September 21, 2006</TD>
  </TR>
  <TR valign="bottom" style="padding-top: 1em">
      <TD align="left" nowrap valign="top">/s/ Youssef El-Zein
  <DIV style="font-size: 1pt; border-bottom: 1px solid #000000">&nbsp;</DIV>
  Youssef El-Zein</TD>
      <TD>&nbsp;</TD>
      <TD align="left">
  Director<BR><BR>
  </TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">September 21, 2006</TD>
  </TR>
  <!-- End Table Body -->
  </TABLE>
  </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">
  
  <DIV align="center">
  <TABLE style="font-size: 10pt" cellspacing="0" border="0" cellpadding="0" width="100%">
  <!-- Begin Table Head -->
  <TR valign="bottom">
      <TD width="30%">&nbsp;</TD>
      <TD width="5%">&nbsp;</TD>
      <TD width="30%">&nbsp;</TD>
      <TD width="5%">&nbsp;</TD>
      <TD width="30%">&nbsp;</TD>
  </TR>
  <TR style="font-size: 10pt" valign="bottom">
      <TD nowrap align="center"><U>Signature</U></TD>
      <TD>&nbsp;</TD>
      <TD nowrap align="center"><U>Title</U></TD>
      <TD>&nbsp;</TD>
      <TD nowrap align="center"><U>Date</U></TD>
  </TR>
  
  <!-- End Table Head -->
  <!-- Begin Table Body -->
  <TR valign="bottom" style="padding-top: 1em"><!-- Blank Space -->
      <TD align="right">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD align="center" nowrap valign="top">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
  </TR>
  <TR valign="bottom" style="padding-top: 1em">
      <TD align="left" nowrap valign="top">/s/ C. Keith Hartley
  <DIV style="font-size: 1pt; border-bottom: 1px solid #000000">&nbsp;</DIV>
  C. Keith Hartley</TD>
      <TD>&nbsp;</TD>
      <TD align="left">
  Director<BR><BR>
  </TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">September 21, 2006</TD>
  </TR>
  <TR valign="bottom" style="padding-top: 1em">
      <TD align="left" nowrap valign="top">/s/ William S. Reardon
  <DIV style="font-size: 1pt; border-bottom: 1px solid #000000">&nbsp;</DIV>
  William S. Reardon</TD>
      <TD>&nbsp;</TD>
      <TD align="left">
  Director<BR><BR>
  </TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">September 21, 2006</TD>
  </TR>
  <TR valign="bottom" style="padding-top: 1em">
      <TD align="left" nowrap valign="top">/s/ Alison Taunton-Rigby
  <DIV style="font-size: 1pt; border-bottom: 1px solid #000000">&nbsp;</DIV>
  Alison Taunton-Rigby, Ph.D.</TD>
      <TD>&nbsp;</TD>
      <TD align="left">
  Director<BR><BR>
  </TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">September 21, 2006</TD>
  </TR>
  <!-- End Table Body -->
  </TABLE>
  </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">
  
  <!-- link1 "INDEX TO EXHIBITS" -->
  <DIV align="left"><A NAME="004"></A></DIV>
  
  <DIV align="center" style="font-size: 10pt; margin-top: 18pt"><B>INDEX TO EXHIBITS</B>
  </DIV>
  
  <DIV align="left">
  <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="3%">&nbsp;</TD>
      <TD width="89%">&nbsp;</TD>
  </TR>
  <TR style="font-size: 8pt" valign="bottom">
  
  <TD nowrap align="center">EXHIBIT<BR><U>NUMBER</U></TD>
      <TD>&nbsp;</TD>
      <TD nowrap align="center"><U>DESCRIPTION</U></TD>
  </TR>
  
  <!-- End Table Head -->
  <!-- Begin Table Body -->
  
  <TR>
      <TD>&nbsp;</TD>
  </TR>
  
  
  <TR valign="bottom">
      <TD align="right" valign="top"><DIV style="margin-left:0px; text-indent:-0px">4.1 (1)
  </DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">Restated Certificate of Incorporation of the Registrant, as amended.</TD>
  </TR>
  <TR valign="bottom"><!-- Blank Space -->
      <TD align="right" 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 align="right" valign="top"><DIV style="margin-left:0px; text-indent:-0px">4.2 (2)
  </DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">Amended and Restated By-laws of the Registrant.</TD>
  </TR>
  <TR valign="bottom"><!-- Blank Space -->
      <TD align="right" 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 align="right" valign="top"><DIV style="margin-left:0px; text-indent:-0px">4.3 (3)
  </DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">Rights Agreement dated
  December&nbsp;10, 2001 between the Registrant and Mellon Investor Services LLC, as rights agent.
  </TD>
  </TR>
  <TR valign="bottom"><!-- Blank Space -->
      <TD align="right" 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 align="right" valign="top"><DIV style="margin-left:0px; text-indent:-0px">4.4 (4)
  </DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top"> Amendment No.&nbsp;1 to Rights
  Agreement dated as of August&nbsp;27, 2003 between the Registrant and Mellon Investor Services LLC.
  </TD>
  </TR>
  <TR valign="bottom"><!-- Blank Space -->
      <TD align="right" 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 align="right" valign="top"><DIV style="margin-left:0px; text-indent:-0px">4.5 (5)
  </DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">Amendment No.&nbsp;2 to Rights
  Agreement dated as of March&nbsp;24, 2006 between the Registrant and Mellon Investor Services LLC.</TD>
  </TR>
  <TR valign="bottom"><!-- Blank Space -->
      <TD align="right" 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 align="right" valign="top"><DIV style="margin-left:0px; text-indent:-0px">5.1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
  </DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">Opinion of Wilmer Cutler Pickering Hale and Dorr LLP.</TD>
  </TR>
  <TR valign="bottom"><!-- Blank Space -->
      <TD align="right" 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 align="right" valign="top"><DIV style="margin-left:0px; text-indent:-0px">23.1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
  </DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">Consent of Ernst &#038; Young LLP.
  </TD>
  </TR>
  <TR valign="bottom"><!-- Blank Space -->
      <TD align="right" 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 align="right" valign="top"><DIV style="margin-left:0px; text-indent:-0px">23.2&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
  </DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">Consent of Wilmer Cutler Pickering
  Hale and Dorr LLP, included in Exhibit&nbsp;5.1 filed herewith.</TD>
  </TR>
  <TR valign="bottom"><!-- Blank Space -->
      <TD align="right" 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 align="right" valign="top"><DIV style="margin-left:0px; text-indent:-0px">24.1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
  </DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">Power of Attorney (See signature page of this Registration Statement).</TD>
  </TR>
  <!-- End Table Body -->
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      <TD width="96"></TD>
  </TR>
  
  <TR valign="top">
      <TD nowrap align="left">(1)</TD>
      <TD>&nbsp;</TD>
      <TD>Previously filed with the Securities and Exchange Commission as an Exhibit to the
  Registrant&#146;s Quarterly Report on Form 10-Q, for the quarter ended June&nbsp;30, 2006 (File No.
  001-31918) and incorporated herein by reference.</TD>
  </TR>
  
  <TR style="font-size: 3pt"><TD>&nbsp;</TD></TR>
  
  <TR valign="top">
      <TD nowrap align="left">(2)</TD>
      <TD>&nbsp;</TD>
      <TD>Previously filed with the Securities and Exchange Commission as an Exhibit to the
  Registrant&#146;s Registration Statement on Form S-1, dated November&nbsp;6, 1995, as amended (File No.
  33-99024) and incorporated herein by reference.</TD>
  </TR>
  
  <TR style="font-size: 3pt"><TD>&nbsp;</TD></TR>
  
  <TR valign="top">
      <TD nowrap align="left">(3)</TD>
      <TD>&nbsp;</TD>
      <TD>Previously filed with the Securities and Exchange Commission as an Exhibit to the
  Registrant&#146;s Registration Statement on Form S-2, dated October&nbsp;10, 2003 (File No.&nbsp;333-109630)
  and incorporated herein by reference.</TD>
  </TR>
  
  <TR style="font-size: 3pt"><TD>&nbsp;</TD></TR>
  
  <TR valign="top">
      <TD nowrap align="left">(4)</TD>
      <TD>&nbsp;</TD>
      <TD>Previously filed with the Securities and Exchange Commission as an Exhibit to the
  Registrant&#146;s Current Report on Form 8-K, dated August&nbsp;29, 2003 (File No.&nbsp;000-27352) and
  incorporated herein by reference.</TD>
  </TR>
  
  <TR style="font-size: 3pt"><TD>&nbsp;</TD></TR>
  
  <TR valign="top">
      <TD nowrap align="left">(5)</TD>
      <TD>&nbsp;</TD>
      <TD>Previously filed with the Securities and Exchange Commission as an Exhibit to the
  Registrant&#146;s Current Report on Form 8-K, dated March&nbsp;29, 2006 (File No.&nbsp;001-31918) and
  incorporated herein by reference.</TD>
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text: sv8
  Table of Contents
  As filed with the Securities and Exchange Commission on September 29, 2006
  Registration No. 333-_____
  SECURITIES AND EXCHANGE COMMISSION
  Washington, D.C. 20549
  FORM S-8
  REGISTRATION STATEMENT UNDER
  THE SECURITIES ACT OF 1933
  Idera Pharmaceuticals, Inc.
  (Exact Name of Registrant as Specified in Its Charter)
  Delaware
  (State or Other Jurisdiction of
  Incorporation or Organization)
  04-3072298
  (I.R.S. Employer
  Identification No.)
  345 Vassar Street
  Cambridge, Massachusetts
  (Address of Principal Executive Offices)
  02139
  (Zip Code)
  2005 Stock Incentive Plan
  (Full Title of the Plan)
  Sudhir Agrawal, D. Phil.
  Chief Executive Officer
  Idera Pharmaceuticals, Inc.
  345 Vassar Street
  Cambridge, Massachusetts 02139
  (Name and Address of Agent For Service)
  (617) 679-5500
  (Telephone Number, Including Area Code, of Agent For Service)
  CALCULATION OF REGISTRATION FEE
  Title of Securities
  Amount to be
  Proposed
  Maximum
  Offering Price
  Proposed
  Maximum
  Aggregate
  Amount of
  Registration
  to be Registered
  Registered(1)
  Per Share
  Offering Price
  Fee
  Common Stock,
  $0.001 par value
  per share
  (including the
  associated
  Preferred Stock
  Purchase Rights)
  500,000 shares
  $3.43(2)
  $1,715,000(2)
  $183.51
  (1)
  In accordance with Rule 416 under the Securities Act of 1933, as amended, this
  registration statement shall be deemed to cover any additional securities that may from time
  to time be offered or issued to prevent dilution resulting from stock splits, stock dividends
  or similar transactions.
  (2)
  Estimated solely for the purpose of calculating the registration fee pursuant to Rules 457(c)
  and 457(h) of the Securities Act of 1933, as amended, and based upon the average of the high
  and low prices of the Registrant's common stock as reported on the American Stock Exchange on
  September 26, 2006.
  TABLE OF CONTENTS
  STATEMENT OF INCORPORATION BY REFERENCE
  Item 5. Interests of Named Experts and Counsel.
  Item 8. Exhibits.
  SIGNATURES
  INDEX TO EXHIBITS
  EX-5.1 OPINION OF WILMER CUTLER PICKERING HALE AND DORR LLP
  EX-23.1 CONSENT OF ERNST AND YOUNG LLP
  Table of Contents
  STATEMENT OF INCORPORATION BY REFERENCE
  This Registration Statement on Form S-8 is filed to register the offer and sale of an
  additional 500,000 shares of the Registrant's common stock, $0.001 par value per share, to be
  issued under the Registrant's 2005 Stock Incentive Plan. This Registration Statement incorporates
  by reference the contents of the registration statement on form S-8, File No. 333-126664, filed by
  the Registrant on July 18, 2005, relating to the Registrant's 2005 Stock Incentive Plan.
  Item 5. Interests of Named Experts and Counsel.
  Wilmer Cutler Pickering Hale and Dorr LLP has opined as to the legality of the securities
  being offered by this registration statement.
  Item 8. Exhibits.
  The Exhibit Index immediately preceding the exhibits is incorporated herein by reference.
  -1-
  Table of Contents
  SIGNATURES
  Pursuant to the requirements of the Securities Act of 1933, as amended, 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 Cambridge, Massachusetts, on September 21,
  2006.
  Idera Pharmaceuticals, Inc.
  By:
  /s/ Sudhir Agrawal
  Sudhir Agrawal, D. Phil.
  Chief Executive Officer
  POWER OF ATTORNEY AND SIGNATURES
  We, the undersigned officers and directors of Idera Pharmaceuticals, Inc., hereby severally
  constitute and appoint Sudhir Agrawal, Robert W. Karr and Robert G. Andersen and each of
  them singly, our true and lawful attorneys with full power to them, and each of them singly, to
  sign for us and in our names in the capacities indicated below, the registration statement on Form
  S-8 filed herewith and any and all subsequent amendments to said registration statement, and
  generally to do all such things in our names and on our behalf in our capacities as officers and
  directors to enable Idera Pharmaceuticals, Inc. to comply with the provisions of the Securities Act
  of 1933, as amended, and all requirements of the Securities and Exchange Commission, hereby
  ratifying and confirming our signatures as they may be signed by our said attorneys, or any of
  them, to said registration statement and any and all amendments thereto.
  Pursuant to the requirements of the Securities Act of 1933, as amended, this registration
  statement has been signed by the following persons in the capacities and on the dates indicated.
  Signature
  Title
  Date
  /s/  James B. Wyngaarden
  James B. Wyngaarden, M.D.
  Chairman of the Board of Directors
  September 21, 2006
  /s/ Sudhir Agrawal
  Sudhir Agrawal, D. Phil
  Chief Executive Officer, Chief
  Scientific Officer and Director
  (Principal Executive Officer)
  September 21, 2006
  /s/ Robert W. Karr
  Robert W. Karr, M.D.
  President and Director
  September 21, 2006
  /s/  Robert G. Andersen
  Robert G. Andersen
  Chief Financial Officer, Vice
  President of Operations,
  Treasurer and Secretary
  (Principal Financial and
  Accounting Officer)
  September 21, 2006
  /s/ Youssef El-Zein
  Youssef El-Zein
  Director
  September 21, 2006
  -2-
  Table of Contents
  Signature
  Title
  Date
  /s/ C. Keith Hartley
  C. Keith Hartley
  Director
  September 21, 2006
  /s/ William S. Reardon
  William S. Reardon
  Director
  September 21, 2006
  /s/ Alison Taunton-Rigby
  Alison Taunton-Rigby, Ph.D.
  Director
  September 21, 2006
  -3-
  Table of Contents
  INDEX TO EXHIBITS
  EXHIBIT
  NUMBER
  DESCRIPTION
  4.1 (1)
  Restated Certificate of Incorporation of the Registrant, as amended.
  4.2 (2)
  Amended and Restated By-laws of the Registrant.
  4.3 (3)
  Rights Agreement dated
  December 10, 2001 between the Registrant and Mellon Investor Services LLC, as rights agent.
  4.4 (4)
  Amendment No. 1 to Rights
  Agreement dated as of August 27, 2003 between the Registrant and Mellon Investor Services LLC.
  4.5 (5)
  Amendment No. 2 to Rights
  Agreement dated as of March 24, 2006 between the Registrant and Mellon Investor Services LLC.
  5.1
  Opinion of Wilmer Cutler Pickering Hale and Dorr LLP.
  23.1
  Consent of Ernst & Young LLP.
  23.2
  Consent of Wilmer Cutler Pickering
  Hale and Dorr LLP, included in Exhibit 5.1 filed herewith.
  24.1
  Power of Attorney (See signature page of this Registration Statement).
  (1)
  Previously filed with the Securities and Exchange Commission as an Exhibit to the
  Registrant's Quarterly Report on Form 10-Q, for the quarter ended June 30, 2006 (File No.
  001-31918) and incorporated herein by reference.
  (2)
  Previously filed with the Securities and Exchange Commission as an Exhibit to the
  Registrant's Registration Statement on Form S-1, dated November 6, 1995, as amended (File No.
  33-99024) and incorporated herein by reference.
  (3)
  Previously filed with the Securities and Exchange Commission as an Exhibit to the
  Registrant's Registration Statement on Form S-2, dated October 10, 2003 (File No. 333-109630)
  and incorporated herein by reference.
  (4)
  Previously filed with the Securities and Exchange Commission as an Exhibit to the
  Registrant's Current Report on Form 8-K, dated August 29, 2003 (File No. 000-27352) and
  incorporated herein by reference.
  (5)
  Previously filed with the Securities and Exchange Commission as an Exhibit to the
  Registrant's Current Report on Form 8-K, dated March 29, 2006 (File No. 001-31918) and
  incorporated herein by reference.