SecProbe.io

Via Facsimile and U.S. Mail Mail Stop 6010
December 9, 2008
         Ms. Patricia Allen Vice President of Finance and Treasurer Alnylam Pharmaceuticals, Inc. 300 Third Street Cambridge, MA  02142
Re: Alnylam Pharmaceuticals, Inc.
 Form 10-K for the Fiscal Year Ended December 31, 2007  File No. 000-50743

Dear Ms. Allen:
We have reviewed your filing and have the following comments.  In our
comments, we ask you to provide us with  information to better understand your
disclosure.  Where a comment requests you to  revise disclosure, the information you
provide should show us what the revised disc losure will look like and identify the annual
or quarterly filing, as appli cable, in which you intend to fi rst include it.  If you do not
believe that revised disclosure  is necessary, explain the reason in your response.  After
reviewing the information provided, we may raise additional comments and/or request
that you amend your filing.

 Please understand that the purpose of our re view process is to assist you in your
compliance with the applicable disclosure  requirements and to  enhance the overall
disclosure in your filing.  We look forward to  working with you in these respects.  We
welcome any questions you may have about our  comments or on any other aspect of our
review.  Feel free to call us at the telephone numbers listed at the end of this letter.
 Material Agreements

1. We note that you refer to several ag reements throughout your Form 10-K and
proxy statement, most notably the agr eements with Tekmira Pharmaceuticals
Corporation and the Massachusetts Institute  of Technology.  It appears that these
agreements may be material to your business,  but they are not f iled as exhibits to
your Form 10-K.  Please explain why you do not believe that these agreements
are material to your business, or, alternativ ely, please file them as exhibits to your
10-K.

Ms. Patricia Allen
Alnylam Pharmaceuticals, Inc.  December 9, 2008 Page 2
 Strategic Alliances, page 13

2. Please revise your disclosure in this s ection to include the following material
terms:
Roche, pages 13-14
• the other therapeutic areas that Roche may expand the license to and the
amount of additional payments they may receive to do so
• the aggregate development and sales milestone payments
• the expiration date of the last-to-e xpire patent covered under the license
agreement
Novartis, pages 14-15
• aggregate potential research payments and milestone payments
• additional payments to be made by Novartis upon exercise of the
integration option
• explanation of the operation of the integration option
• funding commitments from Novartis for pandemic flu alliance
Biogen Idec, page 16
• aggregate milestone payments
• duration and expiration of the agreement
Isis, page 16
• aggregate developmental and regulator y milestone payments and license
fee
• duration and expiration of the agreement

Intellectual Property Related to Fundamental Aspects and Uses of siRNA and RNAi-
related Mechanisms, page 18
3. Please revise the table in this section to include disclosure of the expiration dates
of the various patents.

Note 11. Significant Agreements
Roche Alliance, page 99
4. Your disclosure states “As future milest ones are achieved, and to the extent they
are within the five year term, the am ounts will be recogn ized as revenue
prospectively over the remaining period of  performance.”  Please revise your
disclosure a) to specify whether and to what extent you recogni ze a portion of the
milestone when achieved including your method for determining the amount recognized and b) to what extent and how you recognize any remaining portion of
the achieved milestone “prospectively over th e remaining period of performance.”
Further, specify the accounting, if different, for the milestones under the other agreements where future milest one payments may be received.

Ms. Patricia Allen
Alnylam Pharmaceuticals, Inc.  December 9, 2008 Page 3
 *    *    *    *

Please respond to these comments within  10 business days or tell us when you
will provide us with a response.   Your letter should key your responses to our comments.
Detailed cover letters greatly facilitate our review.  Please furnish your letter on EDGAR
under the form type label CORRESP.

 We urge all persons who are responsible for the accuracy and adequacy of the
disclosure in the filing to be certain that the filing includes all in formation required under
the Securities Exchange Act of 1934 and th at they have provided all information
investors require for an informed invest ment decision.  Since the company and its
management are in possession of all facts re lating to a company’s disclosure, they are
responsible for the accuracy and adequacy of the disclosures they have made.
  In connection with responding to our co mments, please provide, in your letter, a
statement from the company acknowledging that:
• the company is responsible for the adequacy  and accuracy of the disclosure in the
filing;
• staff comments or changes to disclosure  in response to staff comments do not
foreclose the Commission from taking any action with respect to the filing; and
• the company may not assert staff comme nts as a defense in any proceeding
initiated by the Commission or any person under the federal secu rities laws of the
United States.

In addition, please be advise d that the Division of Enfo rcement has access to all
information you provide to the staff of the Divi sion of Corporation Fi nance in our review
of your filing or in response to our comment on your filing.
Please contact Christine Allen, Staff A ccountant, at (202) 551- 3652 or Lisa
Vanjoske, Assistant Chief Accountant, at  (202) 551-3614 if you have any questions
regarding the processing of your response as well as any questions regarding comments
on the financial statements and related matte rs.  You may contact Michael Rosenthall,
Staff Attorney, at (202) 551-3674 or Jeffrey Ri edler, Associate Director, at (202) 551-
3715 with questions on any of the other commen ts.  In this regard, do not hesitate to
contact me, at (202) 551-3679.

Sincerely,

Jim B. Rosenberg Senior Assistant Chief Accountant