COMMON STOCK PURCHASE AGREEMENT

Exhibit 10.2

COMMON STOCK PURCHASE AGREEMENT

     COMMON STOCK PURCHASE AGREEMENT (this “ Agreement ”) dated as of July 8, 2007, between ALNYLAM PHARMACEUTICALS, INC., a Delaware corporation (the “ Company ”), and ROCHE FINANCE LTD, a Swiss corporation (the “ Purchaser ”).

     WHEREAS, the Company and the Purchaser are simultaneously entering into a License and Collaboration Agreement (the “ Collaboration Agreement ”), and the Company, Alnylam Europe AG, a German stock corporation, and an affiliate of the Purchaser are simultaneously entering into a Stock Purchase Agreement (the “ AG Purchase Agreement ”); and

     WHEREAS, in connection with the transactions contemplated by the Collaboration Agreement and the AG Purchase Agreement, the Purchaser desires to purchase from the Company, and the Company desires to issue and sell to the Purchaser, shares of Common Stock, $0.01 par value per share, of the Company (the “ Common Stock ”).

     NOW, THEREFORE, in consideration of the mutual promises hereinafter set forth and other good and valuable consideration, the receipt of which is hereby acknowledged, the parties hereby agree as follows:

     1.  Purchase and Sale of the Shares .

          (a) Subject to the terms and conditions of this Agreement, at the Closing (as defined in clause (b) below), the Company will issue and sell to the Purchaser, and the Purchaser will purchase from the Company, 1,975,000 shares of Common Stock (the “ Shares ”) for an aggregate purchase price equal to the Purchase Price (as defined below). As used herein, the “ Purchase Price ” means $42,462,500, provided that in the event that the Collar Amount (as defined below) is less than $10.98, the “ Purchase Price ” means the sum of (1) the product of (A) 1,975,000 and (B) the Collar Amount (rounded to the nearest whole cent) plus (2) $11,494,500; and the “ Collar Amount ” means the average of the last reported sales prices for the Common Stock as of the end of regular trading hours as reported on the NASDAQ Global Market for the three consecutive trading day period ending on the trading day that is one trading day prior to the Closing Date. The number of Shares and Collar Amount shall be adjusted to reflect the effect of any reclassification, stock split, reverse split, stock dividend, reorganization, recapitalization or other similar change with respect to the Common Stock occurring after the date hereof and prior to the Closing.

          (b) The closing of the transactions contemplated hereby (the “ Closing ”) shall take place at 10:00 a.m., Eastern time, on such date as the Company and the Purchaser may agree upon (the “ Closing Date ”), which shall be no later than the second business day after satisfaction or waiver of the conditions to the Closing set forth in Section 4 of this Agreement (other than delivery of items to be delivered at the Closing and other than satisfaction of those conditions that by their nature are to be satisfied at the Closing, it being understood that the occurrence of the Closing shall remain subject to the delivery of such items and the satisfaction or waiver of such conditions at the Closing), at the offices of Wilmer Cutler Pickering Hale and Dorr LLP, 60 State Street, Boston, Massachusetts (or remotely via the exchange of documents and signatures),

unless another date, place or time is agreed to in writing by the Purchaser and the Company. At the Closing:

               (i) the Purchaser shall pay the Purchase Price to the Company by wire transfer of immediately available funds to an account designated by the Company; and

               (ii) the Company shall instruct the transfer agent for the Common Stock to issue and promptly deliver to the Purchaser a stock certificate representing the Shares.

     2.  Representations and Warranties of the Company . The Company represents and warrants to the Purchaser that the statements contained in this Section 2 are true and correct as of the date hereof, except as set forth herein or in the disclosure schedule delivered by the Company to the Purchaser dated as of the date of this Agreement (the “ Disclosure Schedule ”).

          (a) Organization and Good Standing . The Company is a corporation duly organized, validly existing and in good standing under the laws of the State of Delaware. The Company has the corporate power and authority to enter into and perform its obligations under this Agreement, to own and operate its properties and assets and to carry on its business as currently conducted and as presently proposed to be conducted.

          (b) Capitalization and Voting Rights .

               (i) The authorized capital stock of the Company as of the date of this Agreement consists of 125,000,000 shares of Common Stock and 5,000,000 shares of preferred stock, par value $0.01 per share (the “ Preferred Stock ”), of which 125,000 shares have been designated Series A Junior Participating Preferred Stock (the “ Series A Preferred Stock ”). As of June 29, 2007, (A) 37,635,786 shares of Common Stock were issued and outstanding and (B) no shares of Preferred Stock were issued or outstanding;

               (ii) Except as set forth in Section 2(b)(ii) of the Disclosure Schedule, as of the date hereof, there are: (A) no outstanding options, warrants, rights (including conversion or preemptive rights) or agreements pursuant to which the Company is or may become obligated to issue, sell or repurchase any shares of its capital stock or any other securities of the Company; (B) no restrictions on the transfer of capital stock of the Company imposed by the Restated Certificate of Incorporation or By-laws of the Company, any agreement to which the Company is a party, or any order of any court or any governmental agency to which the Company is subject; and (C) no cumulative voting rights for any of the Company’s capital stock;

               (iii) As of June 29, 2007, of the authorized Common Stock, 4,782,032 shares have been reserved for issuance upon exercise of outstanding options or other stock-based awards under the Company’s stock incentive and stock purchase plans. Other than as set forth in the preceding sentence or in Section 2.3(b)(iii) of the Disclosure Schedule, there are no other shares of Common Stock reserved for issuance. There is no capital stock of the Company held by the Company. As of the date hereof, all of the Series A Preferred Stock is reserved for issuance under the rights agreement between the Company and Computershare Trust Company (f/k/a Equiserve Trust Company, N.A.), as rights agent, dated as of July 13, 2005 (the “ Shareholder Rights Plan ”), and is the only Preferred Stock reserved for issuance.

               (iv) Except as set forth in the Reports (as defined below) or in Section 2(b)(iv) of the Disclosure Schedule, the Company is not a party to and is not subject to any agreement or understanding relating to, and, to the Company’s knowledge, there is no agreement or understanding between any persons which affects or relates to, the voting of shares of capital stock of the Company or the giving of written consents by any stockholder or director of the Company.

          (c) Authorization and Binding Nature . The execution and delivery by the Company of this Agreement, the performance of all obligations of the Company under this Agreement and the authorization, issuance and delivery of the Shares have been duly authorized by all necessary corporate action on the part of the Company, and this Agreement constitutes a valid and legally binding obligation of the Company enforceable against the Company in accordance with its terms, except (i) as may be limited by applicable bankruptcy, insolvency, reorganization, moratorium and other laws of general application affecting the enforcement of creditors’ rights generally and (ii) as may be limited by laws relating to the availability of specific performance, injunctive relief or other equitable remedies.

          (d) Non-Contravention . The execution, delivery and performance by the Company of this Agreement and compliance with the provisions hereof by the Company will not, with or without the giving of notice or the passage of time or both, (i) violate or conflict with the provisions of the certificate of incorporation or by-laws of the Company, (ii) violate or conflict with any provision of law, statute, ordinance, rule, regulation, judgment, decree, order or award of any court, governmental body or arbitrator applicable to the Company, or (iii) violate or conflict with, or require any consent or other action by any person under, any agreement to which the Company is a party or by which it is bound, except for any such violations or conflicts and any such consents or other actions where the failure to obtain such consents or take such other actions, individually or in the aggregate, are not reasonably likely to have a Material Adverse Effect (as defined below). For purposes of this Agreement, the term “ Material Adverse Effect ” means a material adverse effect on the business, properties, financial condition or results of operations of the Company and its subsidiaries, taken as a whole; provided , however , that none of the following shall constitute, or shall be considered in determining whether there has occurred, a Material Adverse Effect: (1) changes that are the result of general economic or political factors affecting the national, regional or world economy or acts of war or terrorism (except to the extent that such changes have a disproportionate effect on the Company and its subsidiaries, taken as a whole); (2) changes that are the result of factors generally affecting the industries or markets in which the Company operates (except to the extent that such changes have a disproportionate effect on the Company and its subsidiaries, taken as a whole); (3) any adverse change, effect or circumstance, including the termination of any collaboration or license agreements between the Company and any entity listed in Section 2(d) of the Disclosure Schedule or the commencement of litigation by any such entity, in any such case, arising out of or resulting from actions contemplated by the parties in connection with this Agreement or the pendency or announcement of the transactions contemplated by this Agreement; (4) changes in law, rules or regulations or generally accepted accounting principles or the interpretation thereof; (5) any action taken pursuant to or in accordance with this Agreement or at the request of the Purchaser; (6) of and by itself and without regard to any other fact or circumstance, any failure by the Company to meet any published securities analyst estimates of revenues, losses, expenses or cash balances, it being understood that if any failure to meet any such estimates is the result of

what would otherwise constitute a Material Adverse Effect, then the parties acknowledge that a Material Adverse Effect shall be deemed to have occurred notwithstanding this clause (6); and (7) of and by itself without regard to any other fact or circumstance, a decline in the price of the Common Stock, it being understood that if any such decline is the result of what would otherwise constitute a Material Adverse Effect, then the parties acknowledge that a Material Adverse Effect shall be deemed to have occurred notwithstanding this clause (7).

          (e) Governmental Consents . Assuming the accuracy of the Purchaser’s representations contained in Section 3 of this Agreement, no consent, approval, order or authorization of, or registration, qualification, designation, declaration or filing with, any Governmental Authority is required on the part of the Company in order to enable the Company to execute, deliver and perform its obligations under this Agreement, except for such qualifications or filings under applicable securities laws as may be required to be made after the Closing in connection with the transactions contemplated by this Agreement. As used herein, “ Governmental Authority ” shall mean any nation or government, any federal, state, municipal, local, provincial, regional or other political subdivision thereof, and any person exercising executive, legislative, judicial regulatory or administrative functions of or pertaining to government.

          (f) Authorization of Shares . When issued, sold and delivered in accordance with the provisions of this Agreement for the consideration expressed herein, the Shares will be duly authorized, validly issued, fully paid and nonassessable, and will be free of restrictions on transfer other than restrictions under this Agreement and applicable state and federal securities laws.

          (g) SEC Reports and Financial Statements . The Company has previously furnished or made available to the Purchaser (i) its Annual Report on Form 10-K for the fiscal year ended December 31, 2006 as filed with the SEC), and (ii) all other reports filed by the Company with the SEC under Section 13 or subsections (a) and (c) of Section 14 of the Securities Exchange Act of 1934, as amended (the “ Exchange Act ”), from January 1, 2007 through the date of this Agreement (such reports are collectively referred to herein as the “ Reports ”). The Reports constitute all of the documents required to be filed by the Company under Section 13 or subsections (a) and (c) of Section 14 of the Exchange Act with the SEC from January 1, 2007 through the date of this Agreement. The Reports complied in all material respects with the requirements of the Exchange Act and the rules and regulations thereunder when filed. The Reports, when considered together, do not contain any untrue statement of a material fact or omit to state a material fact required to be stated therein or necessary to make the statements therein, in light of the circumstances under which they were made, not misleading. The audited financial statements for the year ended December 31, 2006 and the unaudited financial statements for the quarter ended March 31, 2007 included in the Reports (the “ Financial Statements ”) have been prepared in accordance with U.S. generally accepted accounting principles applied on a consistent basis throughout the periods indicated (except as may be indicated in notes or as permitted by Form 10-Q) and fairly present in all material respects the financial condition and operating results of the Company and its subsidiaries as of the dates, and for the periods, indicated therein (subject, in the case of the unaudited financial statements, to normal year-end audit adjustments). Since December 31, 2006, the Company has conducted its business in the ordinary course, and there has not been any Material Adverse Effect. Since

March 31, 2007, the Company has incurred no liabilities (contingent or otherwise) outside the ordinary course of business that would reasonably be expected to have, individually or in the aggregate, a Material Adverse Effect. Except as disclosed in the Financial Statements, the Company is not a guarantor or indemnitor of any indebtedness of any other person, firm or corporation that would reasonably be expected to have, individually or in the aggregate, a Material Adverse Effect.

          (h) Subsidiaries . Except as set forth in the Reports or in Section 2(h) of the Disclosure Schedule and other than with regards to Alnylam Europe AG:

               (i) The Company does not presently own or control, directly or indirectly, any other corporation, association, partnership, trust, joint venture or other business entity and does not currently own or control, directly or indirectly, any capital stock or other ownership interest, directly or indirectly, in any corporation, association, partnership, trust, joint venture or other entity, other than securities in a publicly traded company or mutual fund held for investment by the Company and consisting of less than five percent of the outstanding capital stock of such company.

               (ii) Each corporation, partnership, joint venture, association and other entity controlled by the Company directly or indirectly through one or more intermediaries (each, a “ Subsidiary ”) is duly organized and existing under the laws of its jurisdiction or organization, is in good standing under such laws and is duly qualified to do business as a foreign corporation in each jurisdiction in which a failure to so qualify would reasonably be expected to have, individually or in the aggregate, a Material Adverse Effect.

               (iii) All the outstanding shares of capital stock of each Subsidiary are validly issued, fully paid and nonassessable, and are owned by the Company free and clear of any encumbrances, other than restrictions under securities laws.

               (iv) There are no options, warrants, convertible securities, or other rights, agreement, arrangements or commitments of any character relating to the capital stock of any Subsidiary.

               (v) No Subsidiary is a member of (nor is any part of its business conducted through) any partnership, nor is it a participant in any joint venture or similar arrangement.

               (vi) There are no voting trust, stockholder agreements, proxies or other agreements or understandings in effect with respect to the voting or transfer of any shares of capital stock of or any other interests in any Subsidiary.

          (i) Litigation . Except as set forth in Section 2(i) of the Disclosure Schedule or in the Reports, there is no action, suit, proceeding or investigation pending or, to the Company’s knowledge, currently threatened against the Company or any subsidiary of the Company that questions the validity of this Agreement or the right of the Company to enter into this Agreement, or to consummate the transactions contemplated hereby, or that could reasonably be expected to have, individually or in the aggregate, a Material Adverse Effect, or result in any change in the current equity ownership of the Company, nor is the Company aware

that there is any basis for the foregoing. To the Company’s knowledge, there are no legal actions or investigations pending or threatened involving the employment by or with the Company of any of the Company’s current or former officers, their use in connection with the Company’s business of any information or techniques allegedly proprietary to any of their former employers, or their obligations under any agreements with prior employers or alleging a violation of any federal, state or local statute or common law relationship with the Company. The Company is not a party to any order, writ, injunction, judgment or decree of any court. There is no action, suit, proceeding or investigation by the Company currently pending or that the Company intends to initiate.

          (j) Employee and Consultant Confidentiality Agreements . Except as set forth in Section 2(j) of the Disclosure Schedule, each employee of, or consultant to, the Company or any of its Subsidiaries, who has or is proposed to have access to material confidential or proprietary information of the Company or any of its Subsidiaries, is a signatory to, and is bound by, an agreement with the Company or one or more of its Subsidiaries relating to nondisclosure, proprietary information and assignment of patent, copyright and other intellectual property rights.

          (k) Proprietary Rights . (i) Except as set forth in the Company’s Public Filings or Section 2(k) of the Disclosure Schedule: (A) to the Company’s knowledge, the Company or one of its Subsidiaries owns, free and clear of any lien or encumbrance, or has a valid license to, or has an enforceable right to use, without the payment of any royalty except pursuant to the Material IP Contracts (as hereinafter defined) listed on Section 2(k)(ii) of the Disclosure Schedule, all U.S. and non-U.S. patents, trade secrets, know-how, trademarks, service marks, copyrights, and other proprietary and intellectual property rights, and all grants and applications with respect to the foregoing (collectively, the “ Proprietary Rights ”) necessary for the conduct of the Company’s business as now conducted, the absence of which would not reasonably be expected to have, individually or in the aggregate, a Material Adverse Effect (such Proprietary Rights owned by or licensed to the Company or any of its Subsidiaries collectively, the “ Company Rights ”); (B) to the Company’s knowledge, the Company’s rights in the Company Rights are valid and enforceable; (C) to the Company’s knowledge, all necessary registration, maintenance and renewal fees in respect of the Company Rights have been paid on time; (D) except as disclosed on the Disclosure Schedule and to the Company’s knowledge, none of the Company or its Subsidiaries have or are infringing or otherwise violating the applicable Proprietary Rights of any person, and have not received any notice or are subject to any actual or threatened proceedings alleging such, except for infringements or other violations that would not reasonably be expected to have, individually or in the aggregate, a Material Adverse Effect; (E) the Company and its Subsidiaries have taken reasonable measures to protect the Company Rights, consistent with prudent commercial practices in the biotechnology industry; (F) other than the Material IP Contracts, there are no outstanding material options, licenses or agreements of any kind relating or affecting to the Company Rights except for options, licenses or agreements specifically referenced in the Collaboration Agreement; and (G) there are no breaches or defaults of, or any disputes or threatened disputes concerning, any of the Material IP Contracts, except for breaches, defaults and disputes in Material IP Contracts which are not and will not be sublicensed to F. Hoffmann-La Roche Ltd, a Swiss corporation, and Hoffmann-La Roche Inc., a New Jersey corporation, pursuant to the Collaboration Agreement and which

defaults and disputes would not reasonably be expected to have, individually or in the aggregate, a Material Adverse Effect.

               (ii) Section 2(k)(ii) of the Disclosure Schedule contains a complete and accurate list of all material agreements granting any rights (whether to or by the Company or any of its Subsidiaries) with respect to any of the Company Rights (collectively, the “Material IP Contracts”), specifically indicating, as applicable, each amendment thereto.

          (l) Tax Returns, Payments and Elections . The Company has filed all material tax returns and reports as required, and within the time prescribed, by law. These returns and reports are true and correct in all material respects. The Company has paid or made provision for the payment of all accrued and unpaid taxes and other charges to which the Company is subject and which are not currently due and payable. The federal income tax returns of the Company have never been audited by the Internal Revenue Service, and the Company has not agreed to an extension of the statute of limitations with respect to any of its tax years. Neither the Internal Revenue Service nor any other taxing authority is now asserting against the Company any deficiency or claim for additional material taxes or interest thereon or penalties in connection therewith. The Company has not made any elections pursuant to the U.S. Internal Revenue Code of 1986, as amended (the “ Code ”) (other than elections which relate solely to methods of accounting, depreciation or amortization) which would reasonably be expected to have, individually or in the aggregate, a Material Adverse Effect.

          (m) Insurance . The Company has in full force and effect fire, casualty and liability insurance policies, with coverage, in the case of property insurance, sufficient in amount (subject to reasonable deductibles) to allow it to replace any of its properties that might be damaged or destroyed, and in the case of casualty and liability insurance, in amounts customary for businesses similar to the business of the Company.

          (n) Key Employees . The Company is not aware that any person listed on Section 2(n) of the Disclosure Schedule intends to terminate his or her employment with the Company, nor does the Company have a present intention to terminate the employment of any of the foregoing.

          (o) Real Property Holding Corporation . The Company is not, and has not been during the applicable period specified in Section 897 of the Code, a United States real property holding corporation, as defined in Section 897 of the Code.

          (p) Offering . Subject to the accuracy of the Purchaser’s representations set forth in Section 3 of this Agreement, the offer, sale and issuance of the Shares to be issued in conformity with the terms of this Agreement constitute transactions which are exempt from registration requirements under the Securities Act of 1933, as amended (the “ Securities Act ”) and from all applicable state registration or qualification requirements, other than those with which the Company has complied or will comply with prior to the Closing.

          (q) Licenses and Other Rights; Compliance with Laws . The Company has all franchises, permits, licenses and other rights and privileges from Governmental Authorities necessary to permit it to own its properties and to conduct its business as presently conducted

and is in compliance in all material respects thereunder. The Company and its subsidiaries are in compliance with all laws and governmental rules and regulations applicable to its business, properties and assets, including, without limitation, all such rules, laws and regulations relating to the environment, fair employment practices, the rules, regulations and requirements of the NASDAQ Global Market relating to the continued listing of the Common Stock and occupational safety and health and public safety, except for any non-compliance that would not reasonably be expected to have, individually or in the aggregate, a Material Adverse Effect.

          (r) Brokers . The Company has not incurred, nor will incur, directly or indirectly, as a result of any action taken by the Company, any liability for brokerage or finders’ fees or agents’ commissions or any similar charges in connection with this Agreement or any transaction contemplated hereby.

     3.  Representations and Warranties of the Purchaser . The Purchaser represents and warrants to the Company that the statements contained in this Section 3 are true and correct as of the date hereof.

          (a) Corporate Power . The Purchaser has the corporate power and authority to enter into and perform its obligations under this Agreement. The Purchaser has not been organized, reorganized or recapitalized for the purpose of investing in the Company.

          (b) Authorization and Binding Nature . The execution and delivery by the Purchaser of this Agreement and the performance of all obligations of the Purchaser under this Agreement have been duly authorized by all requisite corporate action on the part of the Purchaser, and this Agreement constitutes a valid and legally binding obligation of the Purchaser, enforceable against the Purchaser in accordance with its terms, except (i) as may be limited by applicable bankruptcy, insolvency, reorganization, moratorium and other laws of general application affecting the enforcement of creditors’ rights generally and (ii) as may be limited by laws relating to the availability of specific performance, injunctive relief or other equitable remedies. No consent, approval, order or authorization of, or registration, qualification, designation, declaration or filing with, any Governmental Authority is required on the part of the Purchaser in connection with the consummation of the transactions contemplated by this Agreement.

          (c) Non-Contravention . The execution, delivery and performance by the Purchaser of this Agreement and compliance with the provisions hereof by the Purchaser will not, with or without the giving of notice or the passage of time or both, (i) violate or conflict with the provisions of the certificate of incorporation or bylaws or other constituent documents of the Purchaser, (ii) violate or conflict with any provision of law, statute, ordinance, rule, regulation, judgment, decree, order or award of any court, governmental body or arbitrator applicable to the Purchaser, or (iii) violate or conflict with any material agreement to which the Purchaser is a party or by which it is bound.

          (d) Accredited Investor . The Purchaser is an “accredited investor,” as defined in Rule 501 under the Securities Act.

          (e) Investment . The Purchaser is acquiring the Shares for its own account for investment, not for resale to any other person and not with a view to or in connection with any resale or distribution. The Purchaser understands that the Shares have not been registered under the securities laws of the United States or any other jurisdiction and cannot be transferred or resold except as permitted pursuant to a valid registration statement or an applicable exemption from registration. The Purchaser acknowledges that the Company has not made any representations with respect to registration of the Shares under applicable securities laws, that there can be no assurance that any market for the Common Stock will continue into the foreseeable future and that, as a result, the Purchaser must be prepared to bear the economic risk of its investment for an indefinite period of time.

          (f) Access to Information . The Purchaser has substantial knowledge and experience in making investment decisions of this type and is capable of evaluating the merits and risks of its investment in the Company. The Company has made available to the Purchaser all documents, some in redacted form, and other information that the Purchaser has concluded is necessary, desirable and appropriate to evaluate the merits and risks of its investment in the Company. The Company has made available to the Purchaser the documents, some in redacted form, requested by the Purchaser, other than those documents requested by the Purchaser but only made available to the Purchaser in redacted form, and has provided answers to all of its questions relating to an investment in the Company. In evaluating the suitability of an investment in the Company, the Purchaser has not relied upon any representations (whether oral or written) other than as set forth herein. The Purchaser has had an opportunity to discuss this investment with representatives of the Company and to ask questions of them. The Purchaser understands that an investment in the Company involves significant risks. The Purchaser understands that, in connection with the transactions contemplated by this Agreement, the Company has offered to issue and sell shares of Common Stock to Novartis Pharma AG under the terms of the Investor Rights Agreement, dated as of September 6, 2005, between the Company and Novartis Pharma AG (the “ NVS Agreement ”).

     4.  Conditions to Closing .

          (a) Conditions to Obligation of the Purchaser . The obligation of the Purchaser to effect the transactions contemplated hereby shall be subject to the satisfaction on or prior to the Closing Date of each of the following conditions, any of which may be waived, in writing, by the Purchaser:

               (i)  Representations and Warranties . The representations and warranties of the Company set forth in this Agreement shall be true and correct as of the Closing Date as though made on and as of the Closing Date (except (A) to the extent such representations and warranties are specifically made as of a particular date, in which case such representations and warranties shall be true and correct only as of such date and (B) where the failure to be true and correct (without regard to an