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  <DIV style="font-family: 'Times New Roman',Times,serif">
  
  <P align="center" style="font-size: 10pt">As filed with the
  Securities and Exchange Commission on June&nbsp;3, 2004
  
  
  <div align="right" style="font-size: 10pt">Registration No.&nbsp;333-_____
  </div>
  
  <P><HR size="4" noshade color="#000000" style="margin-top: -5px">
  <HR size="1" noshade color="#000000" style="margin-top: -10px">
  
  
  <P align="center" style="font-size: 12pt"><B>SECURITIES AND EXCHANGE COMMISSION<BR>
  Washington, D.C. 20549</B>
  
  
  <P align="center" style="font-size: 12pt"><B>FORM S-8</B>
  
  
  <P align="center" style="font-size: 12pt"><B>REGISTRATION STATEMENT UNDER<BR>
  THE SECURITIES ACT OF 1933</B>
  
  
  <P align="center" style="font-size: 12pt"><B>Alnylam Pharmaceuticals, Inc.</B>
  
  <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>
  </TD>
      <TD>&nbsp;</TD>
      <TD align="center" valign="top"><B>77-0602661</B></TD>
  </TR>
  
  <TR valign="bottom">
      <TD align="center" valign="top">(State or Other Jurisdiction of Incorporation<BR>
  or Organization)
  </TD>
      <TD>&nbsp;</TD>
      <TD align="center" valign="top">(I.R.S. Employer<BR>
  Identification No.)</TD>
  </TR>
  
  <TR valign="bottom">
      <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>300 Third Street<BR>
  Cambridge, Massachusetts</B>
  </TD>
      <TD>&nbsp;</TD>
      <TD align="center" valign="top"><B>02142</B></TD>
  </TR>
  
  <TR valign="bottom">
      <TD align="center" valign="top">(Address of Principal Executive Offices)
  </TD>
      <TD>&nbsp;</TD>
      <TD align="center" valign="top">(Zip Code)</TD>
  </TR>
  
  <!-- End Table Body --></TABLE>
  </DIV>
  
  
  
  <P align="center" style="font-size: 10pt"><B>2002 Employee, Director and Consultant Stock Plan<BR>
  2003 Employee, Director and Consultant Stock Plan<BR>
  2004 Stock Incentive Plan<BR>
  2004 Employee Stock Purchase Plan</B><BR>
  (Full Title of the Plan)
  
  
  <P align="center" style="font-size: 10pt"><B>John M. Maraganore, Ph.D.<BR>
  President and Chief Executive Officer<BR>
  Alnylam Pharmaceuticals, Inc.<BR>
  300 Third Street<BR>
  Cambridge, Massachusetts 02142</B><BR>
  (Name and Address of Agent For Service)<BR>
  <B>(617)&nbsp;551-8200</B><BR>
  (Telephone Number, Including Area Code, of Agent For Service)
  
  
  <P align="center" style="font-size: 10pt"><B>CALCULATION OF REGISTRATION FEE</B>
  
  <DIV align="center">
  <TABLE style="font-size: 10pt" cellspacing="0" border="0" cellpadding="0" width="100%">
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  </TR><TR style="font-size: 1px" valign="bottom">
      <TD nowrap align="left" colspan="15" style="border-bottom: 3px solid #000000">&nbsp;</TD>
  </TR>
  <TR style="font-size: 8pt" valign="bottom">    <TD width="1%">&nbsp;</TD>
  
      <TD>&nbsp;</TD>
      <TD style="border-right: 1px solid #000000">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD style="border-right: 1px solid #000000">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD nowrap align="center"><B>Proposed Maximum</B></TD>
      <TD style="border-right: 1px solid #000000">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD nowrap align="center"><B>Proposed Maximum</B></TD>
      <TD style="border-right: 1px solid #000000">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD nowrap align="center"><B>&nbsp;</B></TD>
      <TD width="1%">&nbsp;</TD>
  </TR>
  <TR style="font-size: 8pt" valign="bottom">    <TD width="1%">&nbsp;</TD>
  
      <TD nowrap align="center"><B>Title of Securities</B></TD>
      <TD style="border-right: 1px solid #000000">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD nowrap align="center"><B>Amount to be</B></TD>
      <TD style="border-right: 1px solid #000000">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD nowrap align="center"><B>Offering Price</B></TD>
      <TD style="border-right: 1px solid #000000">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD nowrap align="center"><B>Aggregate Offering</B></TD>
      <TD style="border-right: 1px solid #000000">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD nowrap align="center"><B>Amount of</B></TD>
      <TD width="1%">&nbsp;</TD>
  </TR>
  <TR style="font-size: 8pt" valign="bottom">    <TD width="1%">&nbsp;</TD>
  
      <TD nowrap align="center"><B>to be Registered</B></TD>
      <TD style="border-right: 1px solid #000000">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD nowrap align="center"><B>Registered(1)</B></TD>
      <TD style="border-right: 1px solid #000000">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD nowrap align="center"><B>Per Share</B></TD>
      <TD style="border-right: 1px solid #000000">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD nowrap align="center"><B>Price</B></TD>
      <TD style="border-right: 1px solid #000000">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD nowrap align="center"><B>Registration Fee</B></TD>
      <TD width="1%">&nbsp;</TD>
  </TR>
  
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      <TD width="1%" style="border-top: 1px solid #000000">&nbsp;</TD>
                      <TD valign="top" style="border-top: 1px solid #000000"><DIV style="margin-left:0px; text-indent:-0px">Common Stock, $0.01
  par value per share
  </DIV></TD>
      <TD style="border-right: 1px solid #000000; border-top: 1px solid #000000">&nbsp;</TD>
      <TD style="border-top: 1px solid #000000">&nbsp;</TD>
      <TD align="center" valign="bottom" style="border-top: 1px solid #000000">4,151,700 shares(2)
  </TD>
      <TD style="border-right: 1px solid #000000; border-top: 1px solid #000000">&nbsp;</TD>
      <TD style="border-top: 1px solid #000000">&nbsp;</TD>
  
  <TD align="center" valign="bottom" style="border-top: 1px solid #000000">$7.95(3)
  </TD>
      <TD style="border-right: 1px solid #000000; border-top: 1px solid #000000">&nbsp;</TD>
      <TD style="border-top: 1px solid #000000">&nbsp;</TD>
  
  <TD align="center" valign="bottom" style="border-top: 1px solid #000000">$33,006,015(3)
  </TD>
      <TD style="border-right: 1px solid #000000; border-top: 1px solid #000000">&nbsp;</TD>
      <TD style="border-top: 1px solid #000000">&nbsp;</TD>
  
  <TD align="center" valign="bottom" style="border-top: 1px solid #000000">$4,182</TD>
      <TD width="1%" style="border-top: 1px solid #000000">&nbsp;</TD>
  </TR>
  
  <TR style="font-size: 1px" valign="bottom">
      <TD nowrap align="left" colspan="15" style="border-top: 3px solid #000000">&nbsp;</TD>
  </TR>
  
  
  <!-- End Table Body --></TABLE>
  </DIV>
  
  
  
  <P align="center" style="font-size: 10pt">&nbsp;
  </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">
  
  <P>
  <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="right">(1)</TD>
      <TD width="1%">&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>
  
  </TABLE>
  
  
  <P>
  <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="right">(2)</TD>
      <TD width="1%">&nbsp;</TD>
      <TD>Consists of (i)&nbsp;1,403,532 shares issuable under the 2002 Employee,
  Director and Consultant Stock Plan, (ii)&nbsp;853,432 shares issuable under the
  2003 Employee, Director and Consultant Stock Plan; (iii)&nbsp;1,578,947 shares
  issuable under the 2004 Stock Incentive Plan; and (iv)&nbsp;315,789 shares
  issuable under the 2004 Employee Stock Purchase Plan. As of June&nbsp;3, 2004,
  the unissued balance of the shares reserved for issuance under the 2002
  Employee, Director and Consultant Stock Plan (the &#147;2002 Plan&#148;) and the
  2003 Employee, Director and Consultant Stock Plan (the &#147;2003 Plan&#148;), plus
  the number of shares subject to awards granted under the 2002 Plan and
  2003 Plan that expire, terminate or are otherwise cancelled, which
  aggregate amount not to exceed 2,451,315 additional shares, will be
  issuable under the 2004 Stock Incentive Plan.</TD>
  </TR>
  
  </TABLE>
  
  
  <P>
  <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="right">(3)</TD>
      <TD width="1%">&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 Nasdaq National
  Market on June&nbsp;2, 2004.</TD>
  </TR>
  
  </TABLE>
  
  <P align="center" style="font-size: 10pt">&nbsp;
  </DIV>
  
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  <P><TABLE width="100%" border="0" cellpadding="0" cellspacing="0" style="font-size: 10pt">
  
  </TABLE>
  
  <!-- 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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  </TR>
  <TR><TD colspan="9"><A HREF="#000">PART I
  INFORMATION REQUIRED IN THE SECTION 10(a) PROSPECTUS</A></TD></TR>
  <TR><TD></TD><TD colspan="8"><A HREF="#001">Item&nbsp;1. &nbsp; Plan Information.</A></TD></TR>
  <TR><TD></TD><TD colspan="8"><A HREF="#002">Item&nbsp;2. &nbsp; Registrant Information and Employee Plan Annual Information.</A></TD></TR>
  <TR><TD colspan="9"><A HREF="#003">PART II
  INFORMATION REQUIRED IN THE REGISTRATION STATEMENT</A></TD></TR>
  <TR><TD></TD><TD colspan="8"><A HREF="#004">Item&nbsp;3. &nbsp; Incorporation of Documents by Reference.</A></TD></TR>
  <TR><TD></TD><TD colspan="8"><A HREF="#005">Item&nbsp;4. &nbsp; Description of Securities.</A></TD></TR>
  <TR><TD></TD><TD colspan="8"><A HREF="#006">Item&nbsp;5. &nbsp; Interests of Named Experts and Counsel.</A></TD></TR>
  <TR><TD></TD><TD colspan="8"><A HREF="#007">Item&nbsp;6. &nbsp; Indemnification of Directors and Officers.</A></TD></TR>
  <TR><TD></TD><TD colspan="8"><A HREF="#008">Item&nbsp;7. &nbsp; Exemption from Registration Claimed.</A></TD></TR>
  <TR><TD></TD><TD colspan="8"><A HREF="#009">Item&nbsp;8. &nbsp; Exhibits.</A></TD></TR>
  <TR><TD></TD><TD colspan="8"><A HREF="#010">Item&nbsp;9. &nbsp; Undertakings.</A></TD></TR>
  <TR><TD colspan="9"><A HREF="#011">SIGNATURES</A></TD></TR>
  <TR><TD colspan="9"><A HREF="#012">INDEX TO EXHIBITS</A></TD></TR>
  <TR><TD colspan="9"><A HREF="b50778apexv5.txt">EX-5 OPINION OF COUNSEL</A></TD></TR>
  <TR><TD colspan="9"><A HREF="b50778apexv23w2.txt">EX-23.2 CONSENT OF PRICEWATERHOUSECOOPERS LLP</A></TD></TR>
  <TR><TD colspan="9"><A HREF="b50778apexv23w3.txt">EX-23.3 CONSENT OF PRICEWATERHOUSECOOPERS 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 I
  INFORMATION REQUIRED IN THE SECTION 10(a) PROSPECTUS" -->
  <DIV align="left"><A NAME="000"></A></DIV>
  
  <P align="center" style="font-size: 10pt"><B>PART I<BR>
  INFORMATION REQUIRED IN THE SECTION 10(a) PROSPECTUS</B>
  
  <!-- link2 "Item&nbsp;1. &nbsp; Plan Information." -->
  <DIV align="left"><A NAME="001"></A></DIV>
  
  <P align="left" style="font-size: 10pt"><B>Item&nbsp;1. &nbsp; Plan Information.</B>
  
  
  <P align="left" style="font-size: 10pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The information required by Item&nbsp;1 is included in documents sent or given
  to participants in the plans covered by this registration statement pursuant to
  Rule&nbsp;428(b)(1) of the Securities Act of 1933, as amended (the &#147;Securities
  Act&#148;).
  
  <!-- link2 "Item&nbsp;2. &nbsp; Registrant Information and Employee Plan Annual Information." -->
  <DIV align="left"><A NAME="002"></A></DIV>
  
  <P align="left" style="font-size: 10pt"><B>Item&nbsp;2. &nbsp; Registrant Information and Employee Plan Annual Information.</B>
  
  
  <P align="left" style="font-size: 10pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The written statement required by Item&nbsp;2 is included in documents sent or
  given to participants in the plans covered by this registration statement
  pursuant to Rule&nbsp;428(b)(1) of the Securities Act.
  
  <!-- link1 "PART II
  INFORMATION REQUIRED IN THE REGISTRATION STATEMENT" -->
  <DIV align="left"><A NAME="003"></A></DIV>
  
  <P align="center" style="font-size: 10pt"><B>PART II<BR>
  INFORMATION REQUIRED IN THE REGISTRATION STATEMENT</B>
  
  <!-- link2 "Item&nbsp;3. &nbsp; Incorporation of Documents by Reference." -->
  <DIV align="left"><A NAME="004"></A></DIV>
  
  <P align="left" style="font-size: 10pt"><B>Item&nbsp;3. &nbsp; Incorporation of Documents by Reference.</B>
  
  
  <P align="left" style="font-size: 10pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The registrant is subject to the informational and reporting requirements
  of Sections&nbsp;13(a), 14, and 15(d) of the Securities Exchange Act of 1934, as
  amended (the &#147;Exchange Act&#148;), and in accordance therewith files reports, proxy
  statements and other information with the Securities and Exchange Commission
  (the &#147;Commission&#148;). The following documents, which are on file with the
  Commission, are incorporated in this registration statement by reference:
  
  
  <P align="left" style="font-size: 10pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(a)&nbsp;&nbsp;&nbsp;&nbsp;The registrant&#146;s latest annual report filed pursuant to Section 13(a)
  or 15(d) of the Exchange Act or the latest prospectus filed pursuant to Rule
  424(b) under the Securities Act that contains audited financial statements for
  the registrant&#146;s latest fiscal year for which such statements have been filed.
  
  
  <P align="left" style="font-size: 10pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(b)&nbsp;&nbsp;&nbsp;&nbsp;All other reports filed pursuant to Section 13(a) or 15(d) of the
  Exchange Act since the end of the fiscal year covered by the document referred
  to in (a)&nbsp;above.
  
  
  <P align="left" style="font-size: 10pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(c)&nbsp;&nbsp;&nbsp;&nbsp;The description of the securities contained in the registrant&#146;s
  registration statement on Form 8-A filed under the Exchange Act, including any
  amendment or report filed for the purpose of updating such description.
  
  
  <P align="left" style="font-size: 10pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;All documents subsequently filed by the registrant 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 in this registration statement and to
  be part hereof from the date of the filing of such documents. Any statement
  contained in a document incorporated or deemed to be incorporated by reference
  herein shall be deemed to be modified or superseded for the purposes of this
  registration statement to the extent that a statement contained herein or in
  any other subsequently filed document which also is or is deemed to be
  incorporated by reference herein modifies or supersedes such statement. Any
  statement so modified or superseded shall not be deemed, except as so modified
  or superseded, to constitute a part of this registration statement.
  
  <!-- link2 "Item&nbsp;4. &nbsp; Description of Securities." -->
  <DIV align="left"><A NAME="005"></A></DIV>
  
  <P align="left" style="font-size: 10pt"><B>Item&nbsp;4. &nbsp; Description of Securities.</B>
  
  
  <P align="left" style="font-size: 10pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Not applicable.
  
  
  <P align="center" style="font-size: 10pt">-1-
  </DIV>
  
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  <DIV style="font-family: 'Times New Roman',Times,serif">
  <!-- link2 "Item&nbsp;5. &nbsp; Interests of Named Experts and Counsel." -->
  <DIV align="left"><A NAME="006"></A></DIV>
  
  <P align="left" style="font-size: 10pt"><B>Item&nbsp;5. &nbsp; Interests of Named Experts and Counsel.</B>
  
  
  <P align="left" style="font-size: 10pt">&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. Steven D. Singer,
  a partner of Wilmer Cutler Pickering Hale and Dorr LLP, serves as Secretary to
  the registrant.
  
  <!-- link2 "Item&nbsp;6. &nbsp; Indemnification of Directors and Officers." -->
  <DIV align="left"><A NAME="007"></A></DIV>
  
  <P align="left" style="font-size: 10pt"><B>Item&nbsp;6. &nbsp; Indemnification of Directors and Officers.</B>
  
  
  <P align="left" style="font-size: 10pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Section&nbsp;102 of the Delaware General Corporation Law allows a corporation
  to eliminate the personal liability of directors of a corporation to the
  corporation or its stockholders for monetary damages for a breach of fiduciary
  duty as a director, except where the director breached his duty of loyalty,
  failed to act in good faith, engaged in intentional misconduct or knowingly
  violated a law, authorized the payment of a dividend or approved a stock
  repurchase in violation of Delaware corporate law or obtained an improper
  personal benefit. Alnylam has included such a provision in its Certificate of
  Incorporation.
  
  
  <P align="left" style="font-size: 10pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Section&nbsp;145 of the General Corporation Law of Delaware provides that a
  corporation has the power to indemnify a director, officer, employee or agent
  of the corporation and certain other persons serving at the request of the
  corporation in related capacities against amounts paid and expenses incurred in
  connection with an action or proceeding to which he is or is threatened to be
  made a party by reason of such position, if such person shall have acted in
  good faith and in a manner he reasonably believed to be in or not opposed to
  the best interests of the corporation, and, in any criminal proceeding, if such
  person had no reasonable cause to believe his conduct was unlawful; provided
  that, in the case of actions brought by or in the right of the corporation, no
  indemnification shall be made with respect to any matter as to which such
  person shall have been adjudged to be liable to the corporation unless and only
  to the extent that the adjudicating court determines that such indemnification
  is proper under the circumstances.
  
  
  <P align="left" style="font-size: 10pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Our Restated Certificate of Incorporation includes a provision that
  eliminates the personal liability of its directors for monetary damages for
  breach of fiduciary duty as a director, except for liability for any breach of
  the director&#146;s duty of loyalty to Alnylam or its stockholders, for acts or
  omissions not in good faith or that involve intentional misconduct or a knowing
  violation of law, under section 174 of the Delaware General Corporation Law
  regarding unlawful dividends and stock purchases or for any transaction from
  which the director derived an improper personal benefit.
  
  
  <P align="left" style="font-size: 10pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;These provisions are permitted under Delaware law. Our Restated
  Certificate of Incorporation provides that we must indemnify our directors and
  officers to the fullest extent permitted by Delaware law, we may indemnify our
  other employees and agents to the same extent that we indemnified our officers
  and directors, unless otherwise determined by our Board of Directors and we
  must advance expenses, as incurred, to our directors and executive officers in
  connection with a legal proceeding to the fullest extent permitted by Delaware
  law.
  
  
  <P align="left" style="font-size: 10pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The indemnification provisions contained in our Restated Certificate of
  Incorporation and Amended and Restated Bylaws are not exclusive of any other
  rights to which a person may be entitled by law, agreement, vote of
  stockholders or disinterested directors or otherwise.
  
  
  <P align="left" style="font-size: 10pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;In addition, we maintain insurance on behalf of our directors and
  executive officers insuring them against any liability asserted against them in
  their capacities as directors or officers or arising out of such status.
  
  <!-- link2 "Item&nbsp;7. &nbsp; Exemption from Registration Claimed." -->
  <DIV align="left"><A NAME="008"></A></DIV>
  
  <P align="left" style="font-size: 10pt"><B>Item&nbsp;7. &nbsp; Exemption from Registration Claimed.</B>
  
  
  <P align="left" style="font-size: 10pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Not applicable.
  
  
  <P align="center" style="font-size: 10pt">-2-
  </DIV>
  
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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">
  <!-- link2 "Item&nbsp;8. &nbsp; Exhibits." -->
  <DIV align="left"><A NAME="009"></A></DIV>
  
  <P align="left" style="font-size: 10pt"><B>Item&nbsp;8. &nbsp; Exhibits.</B>
  
  
  <P align="left" style="font-size: 10pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The Exhibit&nbsp;Index immediately preceding the exhibits is incorporated herein by reference.
  
  <!-- link2 "Item&nbsp;9. &nbsp; Undertakings." -->
  <DIV align="left"><A NAME="010"></A></DIV>
  
  <P align="left" style="font-size: 10pt"><B>Item&nbsp;9. &nbsp; Undertakings.</B>
  
  
  <P align="left" style="font-size: 10pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1.&nbsp;&nbsp;&nbsp;&nbsp;<U><I>Item&nbsp;</I><I>512(a)</I><I> of Regulation&nbsp;S-K</I></U>. The undersigned registrant hereby
  undertakes:
  
  
  
  <P align="left" style="margin-left:2%; font-size: 10pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(1)&nbsp;&nbsp;&nbsp;To file, during any period in which offers or sales are being
  made, a post-effective amendment to this registration statement:
  
  
  
  <P align="left" style="margin-left:2%; font-size: 10pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
  (i)&nbsp;&nbsp;&nbsp;To include any prospectus required by Section&nbsp;10(a)(3) of the
  Securities Act;
  
  
  
  <P align="left" style="margin-left:2%; font-size: 10pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
  (ii)&nbsp;&nbsp;&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; and
  
  
  
  <P align="left" style="margin-left:2%; font-size: 10pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
  (iii)&nbsp;&nbsp;&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;
  
  
  
  <P align="left" style="margin-left:2%; font-size: 10pt"><I>provided, however, </I>that paragraphs (i)&nbsp;and (ii)&nbsp;do not apply if the
  information required to be included in a post-effective amendment by
  those paragraphs is contained in periodic reports filed with or furnished
  to the Commission by the registrant pursuant to Section&nbsp;13 or Section
  15(d) of the Exchange Act that are incorporated by reference in the
  registration statement.
  
  
  
  <P align="left" style="margin-left:2%; font-size: 10pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(2)&nbsp;&nbsp;&nbsp;That, for the purpose of determining any liability under the
  Securities Act, 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 <I>bona fide </I>offering thereof.
  
  
  
  <P align="left" style="margin-left:2%; font-size: 10pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(3)&nbsp;&nbsp;&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.
  
  
  <P align="left" style="font-size: 10pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;2.&nbsp;&nbsp;&nbsp;&nbsp;<U><I>Item&nbsp;</I><I>512(b)</I><I> of Regulation&nbsp;S-K</I></U>. The undersigned registrant hereby
  undertakes that, for purposes of determining any liability under the Securities
  Act, each filing of the registrant&#146;s annual report pursuant to Section 13(a) or
  Section 15(d) of the Exchange Act that is incorporated by reference in the
  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 <I>bona fide </I>offering thereof.
  
  
  <P align="left" style="font-size: 10pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;3.&nbsp;&nbsp;&nbsp;&nbsp;<U><I>Item&nbsp;</I><I>512(h)</I><I> of Regulation&nbsp;S-K</I></U>. Insofar as indemnification for
  liabilities arising under the Securities Act 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 Securities 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
  
  
  <P align="center" style="font-size: 10pt">-3-
  </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">
  <P align="left" style="font-size: 10pt">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 Securities Act and will be governed by the final adjudication
  of such issue.
  
  
  <P align="center" style="font-size: 10pt">-4-
  </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="011"></A></DIV>
  
  <P align="center" style="font-size: 10pt"><B>SIGNATURES</B>
  
  
  <P align="left" style="font-size: 10pt">&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 the City of Cambridge, Commonwealth of Massachusetts
  on this 3rd day of June, 2004.
  
  
  <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">&nbsp;</TD>
      <TD colspan="3">ALNYLAM PHARMACEUTICALS, INC.<BR>
  &nbsp;</TD>
      <TD>&nbsp;</TD>
  </TR><TR>
      <TD>&nbsp;</TD>
      <TD valign="top">By:&nbsp;&nbsp;</TD>
      <TD colspan="2" style="border-bottom: 1px solid #000000">/s/ John M. Maraganore</TD>
      <TD>&nbsp;</TD>
  </TR><TR>
      <TD>&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD colspan="2">John M. Maraganore, Ph.D.&nbsp;</TD>
      <TD>&nbsp;</TD>
  </TR><TR>
      <TD>&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD colspan="2">President and Chief Executive Officer&nbsp;</TD>
      <TD>&nbsp;</TD>
  </TR>
  <TR>
      <TD colspan="5">&nbsp;</TD>
  </TR>
  </TABLE>
  
  <P align="center" style="font-size: 10pt"><B>POWER OF ATTORNEY AND SIGNATURES</B>
  
  
  
  <P align="left" style="font-size: 10pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;We, the undersigned officers and directors of Alnylam Pharmaceuticals,
  Inc., hereby severally constitute and appoint John M. Maraganore and Barry E.
  Greene, 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 Alnylam 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.
  
  
  <P align="left" style="font-size: 10pt">&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 align="center">
  <TABLE style="font-size: 10pt" cellspacing="0" border="0" cellpadding="0" width="90%">
  <!-- Begin Table Head --><TR valign="bottom">
      <TD width="27%">&nbsp;</TD>
      <TD width="5%">&nbsp;</TD>
      <TD width="37%">&nbsp;</TD>
      <TD width="5%">&nbsp;</TD>
      <TD width="26%">&nbsp;</TD>
  </TR>
  <TR style="font-size: 8pt" valign="bottom">
      <TD nowrap align="center"><B><U>Signature</U></B></TD>
      <TD>&nbsp;</TD>
      <TD nowrap align="center"><B><U>Title</U></B></TD>
      <TD>&nbsp;</TD>
      <TD nowrap align="center"><B><U>Date</U></B></TD>
  </TR>
  
  <!-- End Table Head -->
  <!-- Begin Table Body -->
  
  <TR>
      <TD>&nbsp;</TD>
  </TR>
  <TR>
      <TD>/s/ John M. Maraganore</TD>
  </TR>
  
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px"><HR size="1" noshade>
  John M. Maraganore, Ph.D.
  </DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">President, Chief
  Executive Officer and
  Director (Principal
  executive officer)
  </TD>
      <TD>&nbsp;</TD>
      <TD align="center" valign="top">June&nbsp;3, 2004</TD>
  </TR>
  
  <TR>
      <TD>&nbsp;</TD>
  </TR>
  
  
  <TR valign="bottom">
  
  <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">/s/ Barry E. Greene</DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="right" 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"><HR size="1" noshade>
  Barry E. Greene
  </DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">Chief Operating Officer
  and Treasurer (Principal
  financial and accounting
  officer)
  </TD>
      <TD>&nbsp;</TD>
      <TD align="center" valign="top">June&nbsp;3, 2004</TD>
  </TR>
  
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="right" 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"><HR size="1" noshade>
  Peter Barrett, Ph.D.
  </DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">Director
  </TD>
      <TD>&nbsp;</TD>
      <TD align="center" valign="top">&nbsp;</TD>
  </TR>
  <TR>
      <TD>&nbsp;</TD>
  </TR>
  
  <TR valign="bottom">
  
  <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">/s/ John E. Berriman</DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="right" 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"><HR size="1" noshade>
  John E. Berriman
  </DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">Director
  </TD>
      <TD>&nbsp;</TD>
      <TD align="center" valign="top">June&nbsp;3, 2004</TD>
  </TR>
  
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="right" 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"><HR size="1" noshade>
  John K. Clarke
  </DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">Director
  </TD>
      <TD>&nbsp;</TD>
      <TD align="center" valign="top">&nbsp;</TD>
  </TR>
  
  <!-- End Table Body --></TABLE>
  </DIV>
  
  
  
  <P align="center" style="font-size: 10pt">-5-
  </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="90%">
  <!-- Begin Table Head --><TR valign="bottom">
      <TD width="33%">&nbsp;</TD>
      <TD width="5%">&nbsp;</TD>
      <TD width="37%">&nbsp;</TD>
      <TD width="5%">&nbsp;</TD>
      <TD width="20%">&nbsp;</TD>
  </TR>
  <TR style="font-size: 8pt" valign="bottom">
      <TD nowrap align="center"><B><U>Signature</U></B></TD>
      <TD>&nbsp;</TD>
      <TD nowrap align="center"><B><U>Title</U></B></TD>
      <TD>&nbsp;</TD>
      <TD nowrap align="center"><B><U>Date</U></B></TD>
  </TR>
  
  <!-- End Table Head -->
  <!-- Begin Table Body -->
  <TR>
      <TD>&nbsp;</TD>
  </TR>
  
  <TR>
      <TD>/s/ Paul R. Schimmel</TD>
  </TR>
  
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px"><HR size="1" noshade>
  Paul R. Schimmel, Ph.D.
  </DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">Director
  </TD>
      <TD>&nbsp;</TD>
      <TD align="center" valign="top">June&nbsp;3, 2004</TD>
  </TR>
  <TR>
      <TD>&nbsp;</TD>
  </TR>
  
  <TR valign="bottom">
  
  <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">/s/ Phillip A. Sharp</DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="right" 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"><HR size="1" noshade>
  Phillip A. Sharp, Ph.D.
  </DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">Director
  </TD>
      <TD>&nbsp;</TD>
      <TD align="center" valign="top">June&nbsp;3, 2004</TD>
  <TR>
      <TD>&nbsp;</TD>
  </TR>
  </TR>
  
  <TR valign="bottom">
  
  <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">/s/
  Kevin P. Starr</DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="right" 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"><HR size="1" noshade>
  Kevin P. Starr
  </DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">Director
  </TD>
      <TD>&nbsp;</TD>
      <TD align="center" valign="top">June&nbsp;3, 2004</TD>
  </TR>
  
  <TR>
      <TD>&nbsp;</TD>
  </TR>
  
  
  <TR valign="bottom">
  
  <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">/s/ Christoph H. Westphal</DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="right" 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"><HR size="1" noshade>
  Christoph H. Westphal, M.D., Ph.D.
  </DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">Director
  </TD>
      <TD>&nbsp;</TD>
      <TD align="center" valign="top">June&nbsp;3, 2004</TD>
  </TR>
  
  <!-- End Table Body --></TABLE>
  </DIV>
  
  
  
  <P align="center" style="font-size: 10pt">-6-
  </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="012"></A></DIV>
  
  <P align="center" style="font-size: 10pt"><B>INDEX TO EXHIBITS</B>
  
  <DIV align="center">
  <TABLE style="font-size: 10pt" cellspacing="0" border="0" cellpadding="0" width="75%">
  <!-- Begin Table Head --><TR valign="bottom">
      <TD width="8%">&nbsp;</TD>
      <TD width="5%">&nbsp;</TD>
      <TD width="87%">&nbsp;</TD>
  </TR>
  <TR style="font-size: 8pt" valign="bottom">
      <TD nowrap align="left"><B><U>Number</U></B></TD>
      <TD>&nbsp;</TD>
  
  <TD nowrap align="left"><B><U>Description</U></B></TD>
  </TR>
  
  <!-- End Table Head -->
  <!-- Begin Table Body -->
  
  <TR>
      <TD>&nbsp;</TD>
  </TR>
  
  <TR valign="bottom">
      <TD 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</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:0px; text-indent:-0px">4.2(1)
  </DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">Amended and Restated By-Laws of the Registrant</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:0px; text-indent:-0px">5
  </DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">Opinion of Wilmer Cutler Pickering Hale and Dorr LLP, counsel to the Registrant</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:0px; text-indent:-0px">23.1
  </DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">Consent of Wilmer Cutler Pickering Hale and Dorr LLP (included in Exhibit&nbsp;5)</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:0px; text-indent:-0px">23.2
  </DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">Consent of PricewaterhouseCoopers 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:0px; text-indent:-0px">23.3
  </DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">Consent of PricewaterhouseCoopers
  Gesellschaft mit beschr&#228;nkter Haftung Wirtschaftsp&#252;fungsgesellschaft</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:0px; text-indent:-0px">24
  </DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">Power of attorney (included on the signature pages of this registration statement)</TD>
  </TR>
  
  <!-- End Table Body --></TABLE>
  </DIV>
  
  
  
  
  <P>
  <HR size="1" width="18%" align="left" noshade>
  
  <TABLE width="100%" border="0" cellpadding="0" cellspacing="0" style="font-size: 10pt">
  
  <TR valign="top">
      <TD width="1%" nowrap align="right">(1)</TD>
      <TD width="3%">&nbsp;</TD>
      <TD width="96%">Previously filed with the Securities and Exchange Commission as an
  Exhibit to the Registrant&#146;s Registration Statement on Form S-1, as amended
  (File No.&nbsp;333-113162) and incorporated herein by reference.</TD>
  </TR>
  
  </TABLE>
  
  
  
  
  <P align="center" style="font-size: 10pt">
  </DIV>
  
  
  </BODY>
  </HTML>
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text: sv8
  Table of Contents
  As filed with the
  Securities and Exchange Commission on June 3, 2004
  Registration No. 333-_____
  SECURITIES AND EXCHANGE COMMISSION
  Washington, D.C. 20549
  FORM S-8
  REGISTRATION STATEMENT UNDER
  THE SECURITIES ACT OF 1933
  Alnylam Pharmaceuticals, Inc.
  (Exact Name of Registrant as Specified in Its Charter)
  Delaware
  77-0602661
  (State or Other Jurisdiction of Incorporation
  or Organization)
  (I.R.S. Employer
  Identification No.)
  300 Third Street
  Cambridge, Massachusetts
  02142
  (Address of Principal Executive Offices)
  (Zip Code)
  2002 Employee, Director and Consultant Stock Plan
  2003 Employee, Director and Consultant Stock Plan
  2004 Stock Incentive Plan
  2004 Employee Stock Purchase Plan
  (Full Title of the Plan)
  John M. Maraganore, Ph.D.
  President and Chief Executive Officer
  Alnylam Pharmaceuticals, Inc.
  300 Third Street
  Cambridge, Massachusetts 02142
  (Name and Address of Agent For Service)
  (617) 551-8200
  (Telephone Number, Including Area Code, of Agent For Service)
  CALCULATION OF REGISTRATION FEE
  Proposed Maximum
  Proposed Maximum
  Title of Securities
  Amount to be
  Offering Price
  Aggregate Offering
  Amount of
  to be Registered
  Registered(1)
  Per Share
  Price
  Registration Fee
  Common Stock, $0.01
  par value per share
  4,151,700 shares(2)
  $7.95(3)
  $33,006,015(3)
  $4,182
  Table of Contents
  (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)
  Consists of (i) 1,403,532 shares issuable under the 2002 Employee,
  Director and Consultant Stock Plan, (ii) 853,432 shares issuable under the
  2003 Employee, Director and Consultant Stock Plan; (iii) 1,578,947 shares
  issuable under the 2004 Stock Incentive Plan; and (iv) 315,789 shares
  issuable under the 2004 Employee Stock Purchase Plan. As of June 3, 2004,
  the unissued balance of the shares reserved for issuance under the 2002
  Employee, Director and Consultant Stock Plan (the "2002 Plan") and the
  2003 Employee, Director and Consultant Stock Plan (the "2003 Plan"), plus
  the number of shares subject to awards granted under the 2002 Plan and
  2003 Plan that expire, terminate or are otherwise cancelled, which
  aggregate amount not to exceed 2,451,315 additional shares, will be
  issuable under the 2004 Stock Incentive Plan.
  (3)
  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 Nasdaq National
  Market on June 2, 2004.
  TABLE OF CONTENTS
  PART I
  INFORMATION REQUIRED IN THE SECTION 10(a) PROSPECTUS
  Item 1.   Plan Information.
  Item 2.   Registrant Information and Employee Plan Annual Information.
  PART II
  INFORMATION REQUIRED IN THE REGISTRATION STATEMENT
  Item 3.   Incorporation of 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
  INDEX TO EXHIBITS
  EX-5 OPINION OF COUNSEL
  EX-23.2 CONSENT OF PRICEWATERHOUSECOOPERS LLP
  EX-23.3 CONSENT OF PRICEWATERHOUSECOOPERS LLP
  Table of Contents
  PART I
  INFORMATION REQUIRED IN THE SECTION 10(a) PROSPECTUS
  Item 1.   Plan Information.
  The information required by Item 1 is included in documents sent or given
  to participants in the plans covered by this registration statement pursuant to
  Rule 428(b)(1) of the Securities Act of 1933, as amended (the "Securities
  Act").
  Item 2.   Registrant Information and Employee Plan Annual Information.
  The written statement required by Item 2 is included in documents sent or
  given to participants in the plans covered by this registration statement
  pursuant to Rule 428(b)(1) of the Securities Act.
  PART II
  INFORMATION REQUIRED IN THE REGISTRATION STATEMENT
  Item 3.   Incorporation of Documents by Reference.
  The registrant is subject to the informational and reporting requirements
  of Sections 13(a), 14, and 15(d) of the Securities Exchange Act of 1934, as
  amended (the "Exchange Act"), and in accordance therewith files reports, proxy
  statements and other information with the Securities and Exchange Commission
  (the "Commission"). The following documents, which are on file with the
  Commission, are incorporated in this registration statement by reference:
  (a)    The registrant's latest annual report filed pursuant to Section 13(a)
  or 15(d) of the Exchange Act or the latest prospectus filed pursuant to Rule
  424(b) under the Securities Act that contains audited financial statements for
  the registrant's latest fiscal year for which such statements have been filed.
  (b)    All other reports filed pursuant to Section 13(a) or 15(d) of the
  Exchange Act since the end of the fiscal year covered by the document referred
  to in (a) above.
  (c)    The description of the securities contained in the registrant's
  registration statement on Form 8-A filed under the Exchange Act, including any
  amendment or report filed for the purpose of updating such description.
  All documents subsequently filed by the registrant 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 in this registration statement and to
  be part hereof from the date of the filing of such documents. Any statement
  contained in a document incorporated or deemed to be incorporated by reference
  herein shall be deemed to be modified or superseded for the purposes of this
  registration statement to the extent that a statement contained herein or in
  any other subsequently filed document which also is or is deemed to be
  incorporated by reference herein modifies or supersedes such statement. Any
  statement so modified or superseded shall not be deemed, except as so modified
  or superseded, to constitute a part of this registration statement.
  Item 4.   Description of Securities.
  Not applicable.
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  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. Steven D. Singer,
  a partner of Wilmer Cutler Pickering Hale and Dorr LLP, serves as Secretary to
  the registrant.
  Item 6.   Indemnification of Directors and Officers.
  Section 102 of the Delaware General Corporation Law allows a corporation
  to eliminate the personal liability of directors of a corporation to the
  corporation or its stockholders for monetary damages for a breach of fiduciary
  duty as a director, except where the director breached his duty of loyalty,
  failed to act in good faith, engaged in intentional misconduct or knowingly
  violated a law, authorized the payment of a dividend or approved a stock
  repurchase in violation of Delaware corporate law or obtained an improper
  personal benefit. Alnylam has included such a provision in its Certificate of
  Incorporation.
  Section 145 of the General Corporation Law of Delaware provides that a
  corporation has the power to indemnify a director, officer, employee or agent
  of the corporation and certain other persons serving at the request of the
  corporation in related capacities against amounts paid and expenses incurred in
  connection with an action or proceeding to which he is or is threatened to be
  made a party by reason of such position, if such person shall have acted in
  good faith and in a manner he reasonably believed to be in or not opposed to
  the best interests of the corporation, and, in any criminal proceeding, if such
  person had no reasonable cause to believe his conduct was unlawful; provided
  that, in the case of actions brought by or in the right of the corporation, no
  indemnification shall be made with respect to any matter as to which such
  person shall have been adjudged to be liable to the corporation unless and only
  to the extent that the adjudicating court determines that such indemnification
  is proper under the circumstances.
  Our Restated Certificate of Incorporation includes a provision that
  eliminates the personal liability of its directors for monetary damages for
  breach of fiduciary duty as a director, except for liability for any breach of
  the director's duty of loyalty to Alnylam or its stockholders, for acts or
  omissions not in good faith or that involve intentional misconduct or a knowing
  violation of law, under section 174 of the Delaware General Corporation Law
  regarding unlawful dividends and stock purchases or for any transaction from
  which the director derived an improper personal benefit.
  These provisions are permitted under Delaware law. Our Restated
  Certificate of Incorporation provides that we must indemnify our directors and
  officers to the fullest extent permitted by Delaware law, we may indemnify our
  other employees and agents to the same extent that we indemnified our officers
  and directors, unless otherwise determined by our Board of Directors and we
  must advance expenses, as incurred, to our directors and executive officers in
  connection with a legal proceeding to the fullest extent permitted by Delaware
  law.
  The indemnification provisions contained in our Restated Certificate of
  Incorporation and Amended and Restated Bylaws are not exclusive of any other
  rights to which a person may be entitled by law, agreement, vote of
  stockholders or disinterested directors or otherwise.
  In addition, we maintain insurance on behalf of our directors and
  executive officers insuring them against any liability asserted against them in
  their capacities as directors or officers or arising out of such status.
  Item 7.   Exemption from Registration Claimed.
  Not applicable.
  -2-
  Table of Contents
  Item 8.   Exhibits.
  The Exhibit Index immediately preceding the exhibits is incorporated herein by reference.
  Item 9.   Undertakings.
  1.
  Item
  512(a)
  of Regulation S-K
  . 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;
  (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; and
  (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 paragraphs (i) and (ii) do not apply if the
  information required to be included in a post-effective amendment by
  those paragraphs is contained in periodic reports filed with or furnished
  to the Commission by the registrant pursuant to Section 13 or Section
  15(d) of the Exchange Act that are incorporated by reference in the
  registration statement.
  (2)   That, for the purpose of determining any liability under the
  Securities Act, 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.
  2.
  Item
  512(b)
  of Regulation S-K
  . The undersigned registrant hereby
  undertakes that, for purposes of determining any liability under the Securities
  Act, each filing of the registrant's annual report pursuant to Section 13(a) or
  Section 15(d) of the Exchange Act that is incorporated by reference in the
  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.
  3.
  Item
  512(h)
  of Regulation S-K
  . Insofar as indemnification for
  liabilities arising under the Securities Act 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 Securities 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
  -3-
  Table of Contents
  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 Securities 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 the City of Cambridge, Commonwealth of Massachusetts
  on this 3rd day of June, 2004.
  ALNYLAM PHARMACEUTICALS, INC.
  By:
  /s/ John M. Maraganore
  John M. Maraganore, Ph.D.
  President and Chief Executive Officer
  POWER OF ATTORNEY AND SIGNATURES
  We, the undersigned officers and directors of Alnylam Pharmaceuticals,
  Inc., hereby severally constitute and appoint John M. Maraganore and Barry E.
  Greene, 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 Alnylam 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, this
  registration statement has been signed by the following persons in the
  capacities and on the dates indicated.
  Signature
  Title
  Date
  /s/ John M. Maraganore
  John M. Maraganore, Ph.D.
  President, Chief
  Executive Officer and
  Director (Principal
  executive officer)
  June 3, 2004
  /s/ Barry E. Greene
  Barry E. Greene
  Chief Operating Officer
  and Treasurer (Principal
  financial and accounting
  officer)
  June 3, 2004
  Peter Barrett, Ph.D.
  Director
  /s/ John E. Berriman
  John E. Berriman
  Director
  June 3, 2004
  John K. Clarke
  Director
  -5-
  Table of Contents
  Signature
  Title
  Date
  /s/ Paul R. Schimmel
  Paul R. Schimmel, Ph.D.
  Director
  June 3, 2004
  /s/ Phillip A. Sharp
  Phillip A. Sharp, Ph.D.
  Director
  June 3, 2004
  /s/
  Kevin P. Starr
  Kevin P. Starr
  Director
  June 3, 2004
  /s/ Christoph H. Westphal
  Christoph H. Westphal, M.D., Ph.D.
  Director
  June 3, 2004
  -6-
  Table of Contents
  INDEX TO EXHIBITS
  Number
  Description
  4.1(1)
  Restated Certificate of Incorporation of the Registrant
  4.2(1)
  Amended and Restated By-Laws of the Registrant
  5
  Opinion of Wilmer Cutler Pickering Hale and Dorr LLP, counsel to the Registrant
  23.1
  Consent of Wilmer Cutler Pickering Hale and Dorr LLP (included in Exhibit 5)
  23.2
  Consent of PricewaterhouseCoopers LLP
  23.3
  Consent of PricewaterhouseCoopers
  Gesellschaft mit beschränkter Haftung Wirtschaftspüfungsgesellschaft
  24
  Power of attorney (included on the signature pages of this registration statement)
  (1)
  Previously filed with the Securities and Exchange Commission as an
  Exhibit to the Registrant's Registration Statement on Form S-1, as amended
  (File No. 333-113162) and incorporated herein by reference.