ACHN 2018 Proxy Supplement

Officer since January 2009. Prior to joining Achillion in January 2009, Mr. Truitt was Vice President of Business Development and Product Strategy for Lev Pharmaceuticals, Inc., a biotechnology company, from October 2007 to December 2008. From July 2006 through September 2007, he served as Lev’s Vice President of Sales and Marketing and led the build out of the commercial team and infrastructure in preparation for product launch. From February 2002 to July 2006, Mr. Truitt was Vice President of Sales and Operations at Johnson & Johnson, a pharmaceutical company, where he directed commercial operations at the company’s OraPharma subsidiary. From 2000 to 2002, Mr. Truitt was Vice President of Sales and Operations of OraPharma, Inc., a pharmaceutical company, prior to its acquisition by Johnson & Johnson. Mr. Truitt holds an M.B.A. from St. Joseph’s University, Philadelphia and a B.S. in Marketing from LaSalle University, Philadelphia. Skills and Qualifications: Our Board believes that Mr. Truitt’s detailed knowledge of our company, his business development expertise, his extensive experience in operations and the development and management of a pharmaceutical commercial infrastructure, and overall knowledge of the life sciences industry qualify him to serve on the Board and adds significant value to our Board of Directors. The shares of the Company’s common stock beneficially owned by Mr. Truitt is set forth under the heading “Security Ownership of Certain Beneficial Owners and Management” in the Proxy Statement. Vote Required The two nominees for director named in Proposal 1 and Proposal 5 to receive the highest number of votes FOR election will be elected as directors. This is called a plurality. If your shares are held by your broker in “street name,” and you do not vote your shares, your brokerage firm may not vote your unvoted shares on Proposal 5. Abstentions are not counted for purposes of electing directors. You may: • vote FOR all nominees; • WITHHOLD your vote from all nominees; or • vote FOR one or more nominees and WITHHOLD your vote from one or more nominees. Votes that are withheld will not be included in the vote tally for the election of directors and will not affect the results of the vote. Board Recommendation The Board of Directors believes that the election of Mr. Truitt to serve as a Class III director is in the best interests of Achillion and the best interest of our stockholders and, therefore, recommends a vote FOR Mr. Truitt. VOTING Whether or not you plan to attend the Annual meeting, we hope you will take time to vote your shares. If you are a stockholder of record, you may vote over the Internet or by completing and mailing a proxy card. If your shares are held in “street name,” that is, held for your account by a broker or other nominee, please follow the instructions provided by the holder of record in order for your shares to be voted. Please vote your shares as soon as possible over the Internet or by using the amended proxy card enclosed with this Proxy Supplement if you would like to change your vote or if you have not voted yet. The amended proxy card enclosed with this Supplement differs from the proxy card previously furnished to you with the Proxy Statement, in that the enclosed proxy card includes the name of Mr. Truitt as a nominee in Proposal 5 and does not include the name of Dr. Deshpande as a nominee in Proposal 1. If you have already voted and do not submit new voting instructions, your previously submitted proxy card or voting instructions will be voted at the Annual Meeting with respect to all matters properly brought before the Annual Meeting, but will not be counted in determining the outcome of the election of Mr. Truitt since he is not listed as a nominee on the original proxy card or voting instructions and will be disregarded with respect to the election of Dr. Deshpande since he is no longer standing for re-election to the Board of Directors. In order to vote on Mr. Truitt as a nominee for director, you must submit a vote on Proposal 5. PLEASE NOTE THAT IF YOU SUBMIT NEW VOTING INSTRUCTIONS, SUCH VOTING INSTRUCTIONS WILL REVOKE ALL PRIOR VOTING INSTRUCTIONS, SO IT IS IMPORTANT TO INDICATE YOUR VOTE ON EACH PROPOSAL WHEN SUBMITTING NEW VOTING INSTRUCTIONS. In the absence of specific instructions to the contrary, shares represented by properly executed proxies received by Achillion, including unmarked proxies, will be voted to approve Proposals 1 through 5. In addition, if any other matters properly come before the Annual Meeting, it is the intention of the persons named in the enclosed proxy card to vote the shares they represent as directed by the Board of Directors. We have not received notice of any other matters that may properly be presented at the Annual Meeting.