SecProbe.io

December 2, 2010

John M. Maraganore, Ph.D. Chief Executive Officer Alnylam Pharmaceuticals, Inc. 300 Third Street
Cambridge, MA 02142

Re: Alnylam Pharmaceuticals, Inc.  Form 10-K
Filed February 26, 2010 File No. 000-50743
 Dear Mr. Maraganore:
 We have reviewed your filing and have the following comments.  In some of our
comments, we may ask you to provide us with  information so we may better understand your
disclosure.
 Please respond to this letter within te n business days by providing the requested
information, or by advising us when you will provide the requested response.  If you do not believe our comments apply to your facts and circum stances, please tell us w hy in your response.
 After reviewing the information you provide in response to these comments, we may
have additional comments.
Form 10-K, filed February 26, 2010

Business, page 2

1. We note that you have included as exhibits various license agreements with each of
Cancer Research Technology Limited, Carneg ie Institution of Washington, Cold Spring
Harbor Laboratory, Garching Innovation Gm bH (now known as Max Planck Innovation
GmbH) and The Board of Trustees of the Le land Stanford Junior University.  Please
describe the material terms of each of thes e agreements, including, but not limited to any
payment provisions, a range of royalty rates,  aggregate milestones,  usage restrictions,
exclusivity provisions and durati on and termination provisions.

Kyowa Hakko Kirin, page 20

2. Please file as an exhibit in your 2010 Form 10-K, the license and collaboration agreement
with Kyowa Hakko Kirin dated June 2008. Alterna tively, tell us the basis for your belief
that you are not required to file this agreement pursuant to Item 601(b)(10)(ii)(B) of

John M. Maraganore, Ph.D. Alnylam Pharmaceuticals, Inc.
December 2, 2010 Page 2

Regulation S-K.
Delivery Initiatives, page 24

3. We note that during 2007, you obtained an excl usive worldwide license to the liposomal
delivery formulation technology of Tekmir a for the discovery, development and
commercialization of LNP formulations for th e delivery of RNAi therapeutics, and a non-
exclusive worldwide license to certain liposomal delivery formulation technology of
Protiva Biotherapeutics Inc., for the discove ry, development and commercialization of
certain LNP formulation for the delivery of RNAi therapeutics.  Please provide the material terms of each of these license agre ements with Tekmira and Protiva, including,
but not limited to any payment provisions, a ra nge of royalty rates, aggregate milestones,
usage restrictions and duration and termina tion provisions.  Also, please file these
agreements as exhibits in your 2010 Form 10-K,  or alternativ ely, tell us the basis for your
belief that you are not required to file these agreements pursuant to Item 601(b)(10)(ii)(B) of Regulation S-K.
 Manufacturing, page 39

4. We note that in 2009, you entered into a ma nufacturing and supply agreement with
Tekmira where you are committed to pay Tekmira a minimum of CAD $11.2 million
(representing U.S. $9.2 million at the tim e of execution) through December 2011 for
manufacturing services.  Please file the agr eement as an exhibit in your 2010 Form 10-K,
or alternatively, tell us  the basis for your belief that you are not required  to file the
agreement pursuant to Item 601(b )(10)(ii)(B) of Regulation S-K.

Proxy Statement on Schedule 14A, filed April 20, 2010

2009 Annual Incentive Program, page 26

5. We note that your annual cash incentive award is based on the achievement of corporate
goals and individual objectives.  However, your disc ussion does not disclose the
corporate goals used as part of the determination of annual cash incentive awards.  In addition, while your discussion does disclose individual objectives , it does not quantify
any targeted levels of achievement or actual levels of achievement, where these objectives are quantitative.  Please provide draft disclosure for your 2011 proxy statement which provides your 2010 corporate goals a nd individual objectives  as well as the
targeted levels of achievement.  To the extent that the goals and objectives are quantitative, the discussion of goals and achievements should also be quantitative.  Please also confirm that in your 2011 proxy statement you will discuss the levels of achievement
of the goals and objectives for each Named Executive Officer.

John M. Maraganore, Ph.D. Alnylam Pharmaceuticals, Inc. December 2, 2010 Page 3

Form 10-Q for the Quarterly Period Ended September 30, 2010

Strategic Alliances, page 23

6. We note that in November 2010, you formed a collaboration with Medtronic and CHDI
to advance ALN-HTT.  We also note that in the United States, you have the opportunity
to invest in clinical development through pr oduct launch in return for a proportional share
of the profits, and in Europe, Medtronic is solely responsible for development and
commercialization, and you are eligible to receive milestones and royalties on product
sales, if any.  Please describe the materi al terms of the collaboration agreement,
including, but not limited to the material obl igations and rights of each party to the
agreement, the payment provisions, a range of royalty rates, a ggregate milestones and
duration and termination provision s.  Also, please file the agre ement as an exhibit in your
2010 Form 10-K, or alternatively, tell us the basis for your belief that you are not
required to file the agreement pursuant to Item 601(b)(10)(ii)(B ) of Regulation S-K.

We urge all persons who are responsible for th e accuracy and adequacy of the disclosure
in the filing to be certain that the filing include s the information the Securities Exchange Act of
1934 and all applicable Exchange Act rules requir e.  Since the company and its management are
in possession of all facts relating to a company’s disclosure, they are responsible for the accuracy
and adequacy of the disclosures they have made.
 In responding to our comments, please provi de a written statement from the company
acknowledging that:
• the company is responsible for the adequacy and accuracy of the disclo sure 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 comments as a defense in any proceeding initiated by
the Commission or any person under the federa l securities laws of  the United States.

You may contact Johnny Gharib  at (202) 551-3170 or me at  (202) 551-3715 if you have
any questions.

Sincerely,
       Jeffrey Riedler
Assistant Director