IDIX (MM)

UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

SCHEDULE 14D-9

SOLICITATION/RECOMMENDATION STATEMENT

UNDER SECTION 14(d)(4) OF THE SECURITIES EXCHANGE ACT OF 1934

(Amendment No. 2)

Idenix Pharmaceuticals, Inc.

(Name of Subject Company)

Idenix Pharmaceuticals, Inc.

(Names of Persons Filing Statement)

COMMON STOCK, PAR VALUE $0.001 PER SHARE

(Title of Class of Securities)

45166R204

(CUSIP Number of Class of Securities)

Ronald C. Renaud, Jr.

President and Chief Executive Officer

Idenix Pharmaceuticals, Inc.

320 Bent Street

Cambridge, Massachusetts 02141

(617) 995-9800

With copies to:

Francis J. Aquila

Krishna Veeraraghavan

Sullivan & Cromwell LLP

125 Broad Street

New York, NY 10004

(212) 558-4000

(Name, address, and telephone numbers of person authorized to receive notices and communications

on behalf of the persons filing statement)

This Amendment No. 2 (this “ Amendment ”) to Schedule 14D-9 amends and supplements the Solicitation/Recommendation Statement on Schedule 14D-9 (as amended from time to time, the “ Statement ”) originally filed by Idenix Pharmaceuticals, Inc., a Delaware corporation (the “ Company ”), with the Securities and Exchange Commission (the “ SEC ”) on June 20, 2014, relating to the tender offer by Imperial Blue Corporation, a Delaware corporation (“ Merger Sub ”), and Merck & Co., Inc., a New Jersey corporation (“ Parent ”) , to purchase all of the issued and outstanding shares of the Company’s common stock, par value $0.001 per share, for $24.50 per share, net to the seller in cash, without interest, less any required withholding of taxes, if any, upon the terms and subject to the conditions set forth in the Offer to Purchase, dated June 20, 2014, as amended, and the related Letter of Transmittal, copies of which are attached to the Tender Offer Statement on Schedule TO filed by Parent and Merger Sub with the SEC on June 20, 2014.

Except as otherwise set forth below, the information set forth in the Statement remains unchanged and is incorporated herein by reference as relevant to the items in this Amendment. Capitalized terms used but not defined herein have the meanings ascribed to them in the Statement.

Item 8 is hereby amended and supplemented by adding the following under the first paragraph under the heading “ Certain Litigation ” on page 34 of the Statement:

“On June 26, 2014, a case was filed in the Trial Court of the Commonwealth of Massachusetts, Superior Court Department, for Suffolk County against the Company, its directors, and Parent and Merger Sub, captioned as follows: Bill Lioio, et. al. v. Idenix Pharmaceuticals, Inc., et. al. , Docket No. B.L.S. 14-2010. This case is a putative class action brought by purported stockholders alleging, among other things, that the Company’s directors breached their fiduciary duties by approving the Merger Agreement, and that Parent and Merger Sub aided and abetted these alleged breaches of fiduciary duty. The complaint seeks, among other things, either to enjoin the proposed transaction or to rescind it should it be consummated, as well as money damages.”

SIGNATURE

After due inquiry and to the best of my knowledge and belief, I certify that the information set forth in this Schedule 14D-9 is true, complete and correct.

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