Sec Form 4 Filing - Westphal Christoph H @ ALNYLAM PHARMACEUTICALS INC - 2004-06-03

FORM 4 Check this box if no longer subject to Section 16. Form 4 or Form 5 obligations may continue. See Instruction 1(b).

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 STATEMENT OF CHANGES IN BENEFICIAL OWNERSHIP Filed pursuant to Section 16(a) of the Securities Exchange Act of 1934, Section 17(a) of the Public Utility Holding Company Act of 1935 or Section 30(h) of the Investment Company Act of 1940

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1. Name and Address of Reporting Person Westphal Christoph H 2. Issuer Name and Ticker or Trading Symbol ALNYLAM PHARMACEUTICALS INC [ ALNY] 5. Relationship of Reporting Person(s) to Issuer (Check all applicable) X __ Director X __ 10% Owner _____ Officer (give title below) _____ Other (specify below) (Last) (First) (Middle) C/O POLARIS VENTURE PARTNERS, 1000 WINTER STREET, SUITE 3350 3. Date of Earliest Transaction (MM/DD/YY) 06/03/2004 (Street) WALTHAM, MA02451 4. If Amendment, Date Original Filed (MM/DD/YY) 6. Individual or Joint/Group Filing (Check Applicable Line) __ X __ Form filed by One Reporting Person _____ Form filed by More than One Reporting Person (City) (State) (Zip)

Table I - Non-Derivative Securities Acquired, Disposed of, or Beneficially Owned 1.Title of Security (Instr. 3) 2. Transaction Date (MM/DD/YY) 2A. Deemed Execution Date, if any (MM/DD/YY) 3. Transaction Code (Instr. 8) 4. Securities Acquired (A) or Disposed of (D) (Instr. 3, 4 and 5) 5. Amount of Securities Beneficially Owned Following Reported Transaction(s) (Instr. 3 and 4) 6. Ownership Form: Direct (D) or Indirect (I) (Instr. 4) 7. Nature of Indirect Beneficial Ownership (Instr. 4) Code V Amount (A) or (D) Price Common Stock 06/03/2004 C 62,574 A $ 0 62,574 I See footnotes ( 1 ) ( 6 ) ( 7 ) Common Stock 06/03/2004 C 37,983 A $ 0 37,983 I See footnotes ( 2 ) ( 6 ) ( 7 ) Common Stock 06/03/2004 C 2,409,970 A $ 0 2,409,970 I See footnotes ( 3 ) ( 6 ) ( 7 )

Table II - Derivative Securities Acquired, Disposed of, or Beneficially Owned ( e.g. , puts, calls, warrants, options, convertible securities) 1. Title of Derivative Security (Instr. 3) 2. Conversion or Exercise Price of Derivative Security 3. Transaction Date (MM/DD/YY) 3A. Deemed Execution Date, if any (MM/DD/YY) 4. Transaction Code (Instr. 8) 5. Number of Derivative Securities Acquired (A) or Disposed of (D) (Instr. 3, 4, and 5) 6. Date Exercisable and Expiration Date (MM/DD/YY) 7. Title and Amount of Underlying Securities (Instr. 3 and 4) 8. Price of Derivative Security (Instr. 5) 9. Number of Derivative Securities Beneficially Owned Following Reported Transaction(s) (Instr. 4) 10. Ownership Form of Derivative Security: Direct (D) or Indirect (I) (Instr. 4) 11. Nature of Indirect Beneficial Ownership (Instr. 4) Code V (A) (D) Date Exercisable Expiration Date Title Amount or Number of Shares Series A Convertible Preferred Stock ( 4 ) 06/03/2004 C 24,925 ( 4 ) ( 5 ) Common Stock 13,118 $ 0 0 I See footnotes ( 1 ) ( 6 ) ( 7 ) Series A Convertible Preferred Stock ( 4 ) 06/03/2004 C 15,130 ( 4 ) ( 5 ) Common Stock 7,963 $ 0 0 I See footnotes ( 2 ) ( 6 ) ( 7 ) Series A Convertible Preferred Stock ( 4 ) 06/03/2004 C 959,955 ( 4 ) ( 5 ) Common Stock 505,239 $ 0 0 I See footnotes ( 3 ) ( 6 ) ( 7 ) Series B Convertible Preferred Stock ( 4 ) 06/03/2004 C 90,728 ( 4 ) ( 5 ) Common Stock 47,751 $ 0 0 I See footnotes ( 1 ) ( 6 ) ( 7 ) Series B Convertible Preferred Stock ( 4 ) 06/03/2004 C 55,072 ( 4 ) ( 5 ) Common Stock 28,985 $ 0 0 I See footnotes ( 2 ) ( 6 ) ( 7 ) Series B Convertible Preferred Stock ( 4 ) 06/03/2004 C 3,494,200 ( 4 ) ( 5 ) Common Stock 1,839,052 $ 0 0 I See footnotes ( 3 ) ( 6 ) ( 7 ) Series C Convertible Preferred Stock ( 4 ) 06/03/2004 C 3,240 ( 4 ) ( 5 ) Common Stock 1,705 $ 0 0 I See footnotes ( 1 ) ( 6 ) ( 7 ) Series C Convertible Preferred Stock ( 4 ) 06/03/2004 C 1,967 ( 4 ) ( 5 ) Common Stock 1,035 $ 0 0 I See footnotes ( 2 ) ( 6 ) ( 7 ) Series C Convertible Preferred Stock ( 4 ) 06/03/2004 C 124,791 ( 4 ) ( 5 ) Common Stock 65,679 $ 0 0 I See footnotes ( 3 ) ( 6 ) ( 7 )

Reporting Owners Reporting Owner Name / Address Relationships Director 10% Owner Officer Other Westphal Christoph H C/O POLARIS VENTURE PARTNERS 1000 WINTER STREET, SUITE 3350 WALTHAM, MA02451 X X Signatures /s/ Christoph H. Westphal 06/07/2004 Signature of Reporting Person Date

Explanation of Responses:

( 1 )These shares are owned directly by Polaris Venture Partners Entrepreneurs' Fund III, L.P. Christoph Westphal is a member of Polaris Venture Management Co. III, LLC, the General Partner of Polaris Venture Partners Entrepreneurs' Fund III, L.P. As such, he may be deemed to share voting and investment powers with respect to the shares owned by Polaris Venture Partners Entrepreneurs' Fund III, L.P. He disclaims beneficial ownership of all such shares except to the extent of his proportionate pecuniary interest therein. ( 2 )These shares are owned directly by Polaris Venture Partners Founders' Fund III, L.P. Christoph Westphal is a member of Polaris Venture Management Co. III, LLC, the General Partner of Polaris Venture Partners Founders' Fund III, L.P.. As such, he may be deemed to share voting and investment powers with respect to the shares owned by Polaris Venture Partners Founders' Fund III, L.P. He disclaims beneficial ownership of all such shares except to the extent of his proportionate pecuniary interest therein. ( 3 )These shares are owned directly by Polaris Venture Partners III, L.P. Christoph Westphal is a member of Polaris Venture Management Co. III, LLC, the General Partner of Polaris Venture Partners III, L.P. As, such, he may be deemed to share voting and investmewnt powers with respect to the shares owned by Polaris Venture Partners III, L.P. He disclaims beneficial ownership of all such shares except to the extent of his proportionate pecuniary interest therein. ( 4 )Each share of Series A, B and C Preferred Stock automatically converted into approximately 0.53 shares of common stock upon the closing of the issuer's initial public offering of common stock. ( 5 )N/A ( 6 )North Star Ventures directly or indirectly provides investment advisory services to various venture capital funds, including Polaris Venture Management Co. III, LLC, the General Partner of Polaris Venture Partners Entrepreneurs' Fund III, L.P., Polaris Venture Partners Founders' Fund III, L.P. and Polaris Venture Partners III, L.P. The respective General Partners of these funds exercise sole voting and investment power with respect to the shares held by such funds. ( 7 )Continued from footnote 6. The members of North Star Ventures are members of Polaris Venture Management Co. III, LLC, the General Partner of Polaris Venture Partners Entrepreneurs' Fund III, L.P., Polaris Venture Partners Founders' Fund III, L.P. and Polaris Venture Partners III, L.P. As members of Polaris Venture Management Co. III, LLC, they may be deemed to share voting and investment powers with respect to the shares held by such funds. These principals disclaim beneficial ownership of all such shares except to the extent of their proportionate pecuniary interest therein.

Reminder: Report on a separate line for each class of securities beneficially owned directly or indirectly.

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