June 3, 2004


Alnylam Pharmaceuticals, Inc.
300 Third Street
Cambridge, Massachusetts 02142

     Re:  2002 Employee, Director and Consultant Stock Plan
          2003 Employee, Director and Consultant Stock Plan
          2004 Stock Incentive Plan
          2004 Employee Stock Purchase Plan

Ladies and Gentlemen:

We have assisted in the preparation of a Registration Statement on Form S-8 (the
"Registration Statement") to be filed with the Securities and Exchange
Commission (the "Commission") under the Securities Act of 1933, as amended (the
"Securities Act"), relating to an aggregate of 4,151,700 shares of common stock,
$0.01 par value per share (the "Shares"), of Alnylam Pharmaceuticals, Inc., a
Delaware corporation (the "Company"), issuable under the Company's 2002
Employee, Director and Consultant Stock Plan, the Company's 2003 Employee,
Director and Consultant Stock Plan, the Company's 2004 Stock Incentive Plan and
the Company's 2004 Employee Stock Purchase Plan (collectively, the "Plans").

We have examined the Certificate of Incorporation and By-Laws of the Company,
each as amended and restated to date, and originals, or copies certified to our
satisfaction, of all pertinent records of the meetings of the directors and
stockholders of the Company, the Registration Statement and such other documents
relating to the Company as we have deemed material for the purposes of this
opinion.

In our examination of the foregoing documents, we have assumed the genuineness
of all signatures, the authenticity of all documents submitted to us as
originals, the conformity to original documents of all documents submitted to us
as certified, photostatic or other copies, the authenticity of the originals of
any such documents and the legal competence of all signatories to such
documents.

We assume that the appropriate action will be taken, prior to the offer and sale
of the Shares in accordance with the Plans, to register and qualify the Shares
for sale under all applicable state securities or "blue sky" laws.

We express no opinion herein as to the laws of any state or jurisdiction other
than the state laws of The Commonwealth of Massachusetts, the General
Corporation Law of the State of Delaware and the federal laws of the United
States of America.

It is understood that this opinion is to be used only in connection with the
offer and sale of the Shares while the Registration Statement is in effect.

Please note that we are opining only as to the matters expressly set forth
herein, and no opinion should be inferred as to any other matters.



Based on the foregoing, we are of the opinion that the Shares have been duly
authorized for issuance and, when the Shares are issued and paid for in
accordance with the terms and conditions of the Plans, the Shares will be
validly issued, fully paid and nonassessable.

We hereby consent to the filing of this opinion with the Commission in
connection with the Registration Statement in accordance with the requirements
of Item 601(b)(5) of Regulation S-K under the Securities Act. In giving such
consent, we do not hereby admit that we are in the category of persons whose
consent is required under Section 7 of the Securities Act or the rules and
regulations of the Commission.


Very truly yours,


WILMER CUTLER PICKERING
HALE AND DORR LLP


By: /s/ Peter N. Handrinos
   ----------------------------------
    Peter N. Handrinos, a Partner