Exhibit 23.2

Consent of Ernst & Young LLP, Independent Auditors of Regulus Therapeutics LLC

We consent to the use of our report dated February 23, 2009, with respect to the financial statements of Regulus Therapeutics LLC incorporated by reference into the Registration Statements (Form S-3 Nos. 333-138586, 333-131233, 333-129905, 333-140076 and Form S-8 Nos. 333-127450, 333-116151, 333-148114) and related Prospectus of Alnylam Pharmaceuticals, Inc. included in Alnylam Pharmaceuticals, Inc.’s Annual Report (Form 10-K) for the year ended December 31, 2008.

/s/ Ernst & Young LLP  

San Diego, California
February 23, 2009