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                                                                                               July 8, 2009

Mr. Joshua Boger
Chief Executive Officer
Vertex Pharmaceuticals Incorporated
130 Waverly Street
Cambridge, MA  02139-4242

Re: Vertex Pharmaceuticals Incorporated
Form 10-K for the Period Ended December 31, 2008
Form 10-Q for the Quarterly Period Ended March 31, 2009
Definitive Proxy Statement on Schedule 14A filed April 8, 2009
File No. 000-19319

Dear Mr. Boger:

We have reviewed your filings and have the following comments. In our
comments, we ask you to provide us with  information to better understand your
disclosure. Where a comment requests you to  revise disclosure, the information you
provide should show us what the revised disc losure will look like and identify the annual
or quarterly filing, as ap plicable, in which you intend to firs t include it.    If you disagree,
we will consider your explanation as to why our comments are inapplicable or a revision
is unnecessary.  After reviewing the info rmation provided, we may raise additional
comments and/or request that you amend your filing.

 Please understand that the purpose of our re view process is to assist you in your
compliance with the applicable disclosure  requirements and to  enhance the overall
disclosure in your filing.  We look forward to  working with you in these respects.  We
welcome any questions you may have about our  comments or on any other aspect of our
review.  Feel free to call us at the telephone numbers listed at the end of this letter.

Form 10-K for the Period Ended December 31, 2008

Item 1. Business
Intellectual Property, page 15

1. We note that you disclose that you have the rights to a number of U.S and foreign
patents covering your potential drug targ ets, compounds you are developing to
modulate those targets, methods of making or using those compounds and
proprietary elements of your drug disc overy platform.  Please expand your
disclosure here to include the number of pa tents related to each material potential
drug target, compound, method and/or propr ietary element and the expiration
dates for those patents.

Mr. Joshua Boger
Vertex Pharmaceuticals Incorporated July 8, 2009 Page 2

Management’s Discussion and Analysis of  Financial Conditions and Results of
Operations
Critical Accounting Policies and Estimates, page 55

2. In your discussion regarding the recogniti on of revenue associated with up-front
license fees, you indicate that your estimat es regarding the period of performance
have changed in the past and may change in the future and that any change could
result in substantial changes to th e period over which up- front license fee
revenues are recognized.  Please revise your disclosure to specifically discuss the
magnitude of your historical changes in  estimate and the resulting financial
statement impact as well as the impact of reasonably likely changes in your
current period estimate.

Results of Operations
Research and Development Expenses, page 61

3. We acknowledge your July 30, 2004 response to comment 1 of our June 28, 2004
letter in which you indicated that you did not track research and development
expenses by project.  Please tell us wh ether you have since modified your systems
to track these expenses by project.  If  so, please revise your  disclosure to add
discussion of these expenses by project.  If not, please specifically disclose that
fact, explain why you do not maintain and evaluate research and development
costs by project and provide other quantitative or quali tative disclosure that
indicates the amount of the company’s re sources being used on each project.

Definitive Proxy Statement on Schedule 14A filed April 8, 2009

Compensation Discussion and Analysis
2008 Compensation Decisions for Perf ormance-Based Elements, page 29

4. You disclose that you “consider aspects of [your] annual corp orate goals to be
confidential information and closely guard this information.”  Please
supplementally describe the “aspects of [your] corporate goals” that you believe
constitute confidential in formation.  Please present a comprehensive analysis
supporting your conclusion that the disclosure  of this information is not material
to investors and would cause competitive harm if it is disclosed.  Additionally,
when information regarding targets and goals is not provide d on the basis that
disclosure would cause competitive harm, you must discuss how difficult it will
be for the executive or how likely it will be for your company to achieve the
undisclosed targets or goals. Please see In struction 4 to Item 402(b) of Regulation
S-K.  Please note that you may request c onfidential treatment for portions of your
analysis pursuant to Rule 83.

Mr. Joshua Boger
Vertex Pharmaceuticals Incorporated July 8, 2009 Page 3
 Form 10-Q for the Quarterly Period Ended March 31, 2009

Note 9.  Acquisition of ViroChem Pharma Inc.

Purchase Price, page 18

5. Please revise your disclosure to descri be the primary reasons for the business
combination and the factors that make up the goodwill recognized.  Refer to
paragraphs 68d and 68e  of SFAS 141(R).

Preliminary Allocation of Asse ts and Liabilities, page 18

6. Please revise your disclosure to indi cate when you expect  to finalize your
valuations of the intangible assets acquired.

7. You disclose that the $525.9 million of inta ngible assets in your preliminary fair
value estimates at the acquisition date rela te entirely to in-process research and
development, or IPR&D, assets.  Please address the following comments:
a. You disclose that your IPR&D assets primarily relate to ViroChem’s two
polymerase inhibitors, VCH-222 and VCH-759.  On page 32, you indicate
that you would incur signif icant charges if, in particular VCH-222, were to
become impaired.  Consistent with the guidance in paragraph 4.2.03 of the
AICPA Practice Aid on IPR&D, please revise  your disclosure related to these
IPR&D assets here and in MD&A to:
• Indicate separately the values of VCH-222 and VCH-759;
• Clarify the differences between th e two projects and why VCH-222 is
apparently more valuable than VCH-759;
• Indicate the nature, timing and estimate d costs of the efforts necessary to
complete the projects, and the anticipated completion dates;
• Disclose significant appraisal assumptions, such as:
o The period in which material net cash inflows from significant projects
are expected to commence;
o Material anticipated changes from  historical expense levels; and
o The risk adjusted discount rate applied to each project’s cash flows.
• Discuss in periods after the acquisition the status of efforts to complete the
projects, and the impact of any delays  on your expected investment return,
results of operations and financial condition.
b. Please explain to us why you did not iden tify any other intangible assets at
acquisition.  In your respons e, please specifically indi cate why you apparently
do not believe that you acquired core  technologies for which you have
alternative future uses in research an d development, or otherwise.  Also,
please specifically explain why you appa rently do not identify any of the
technology-based intangible assets indicated in paragraph A51 of SFAS
141(R). Please reference for us the au thoritative literature you rely upon to
support your accounting.
c. On page 30 you indicate that you are evaluating ViroChem’s non-HCV
programs and that you may seek to license  rights to ViroChem’s other assets
to a third-party collaborator.   Plea se explain to us how you accounted for

Mr. Joshua Boger
Vertex Pharmaceuticals Incorporated July 8, 2009 Page 4
 these programs and assets in your acqui sition accounting and reference for us
the authoritative literature you rely  upon to support your accounting.

*    *    *    *

Please respond to these comments within  10 business days or tell us when you
will provide us with a response.  Please furnish a letter that  keys your responses to our
comments and provides the requested information.  Detailed letters greatly facilitate our
review.  Please furnish your letter on EDGAR under the form type label CORRESP.

 We urge all persons who are responsible for the accuracy and adequacy of the
disclosure in the filing to be certain that the filing includes all in formation required under
the Securities Exchange Act of 1934 and th at they have provided all information
investors require for an informed invest ment decision.  Since the company and its
management are in possession of all facts re lating to a company’s disclosure, they are
responsible for the accuracy and adequacy of the disclosures they have made.

 In connection with responding to our co mments, please provide, in your letter, a
statement from the company acknowledging that:

• the company is responsible for the adequacy  and accuracy of the disclosure in the
filing;
• staff comments or changes to disclosure  in response to staff comments do not
foreclose the Commission from taking any action with respect to the filing; and
• the company may not assert staff comme nts as a defense in any proceeding
initiated by the Commission or any person under the federal secu rities laws of the
United States.

In addition, please be advise d that the Division of Enfo rcement has access to all
information you provide to the staff of the Divi sion of Corporation Fi nance in our review
of your filing or in response to our comments on your filing.

Please contact Kei Ino, Staff Accountant,  at (202) 551-3659 or  Mark Brunhofer,
Senior Staff Accountant, at (202) 551-3638 if you have  questions regarding the
processing of your response as well as any questions regarding comments on the financial
statements and related matters.  You may c ontact Mike Rosenthall, Staff Attorney at
(202) 551-3674 or Jennifer Riegel, Staff Atto rney at (202) 551-3575 with questions on
any of the other comments.  In this regard, do not hesitate to cont act me, at (202) 551-
3679.

Sincerely,

Jim B. Rosenberg
Senior Assistant Chief Accountant