Exhibit 10.1


VERTEX PHARMACEUTICALS INCORPORATED


EMPLOYEE STOCK PURCHASE PLAN


(as amended and restated


May 31,
2007)


ARTICLE 1


PURPOSE AND
DEFINITIONS


 SECTION 1.1.  PURPOSE. 
The purpose of the Vertex Pharmaceuticals Incorporated Employee Stock
Purchase Plan is to provide employees with an opportunity to purchase Common
Stock in the Company through payroll deductions, thereby encouraging employees
to share in the economic growth and success of the Company through stock
ownership.


 SECTION 1.2.  DEFINITIONS. 
Whenever used in the Plan, unless the context clearly indicates
otherwise, the following terms shall have the following meanings:


(a)                                “BENEFICIARY” with respect to a Participant, means
the beneficiary designated by the Participant under the group term life
insurance plan maintained by the Company or such other beneficiary as may be
designated by a Participant for purposes of this Plan.


(b)                               “BOARD OF DIRECTORS” means the Board of Directors
of the Company.


(c)                                “CODE” means the Internal Revenue Code of 1986, as
the same may be amended from time to time, and references thereto shall include
the valid Treasury regulations issued thereunder.


(d)                               “COMMITTEE” means the Management Development and
Compensation Committee of the Board of Directors or such other committee of the
Board of Directors designated by the 
Board of Directors to administer the Company’s equity compensation
plans.


(e)                                “COMMON STOCK” means shares of the $.01 par value
common stock of the Company and any other stock or securities resulting from the
adjustment thereof or substitution therefor as described in Section 3.4.


(f)                                  “COMPANY” means Vertex Pharmaceuticals
Incorporated or any successor by merger, purchase, or otherwise.


(g)                               “COMPENSATION” means the cash compensation
received by an Employee for services, including pre-tax employee compensation
made to the Company’s 401(k) savings plan, but not including overtime or
bonuses.


(h)                               “EFFECTIVE DATE” means July 1, 1992.


(i)                                   “ELECTION” means an election by a Participant to
terminate an Offering Period on the first Purchase Date of such Offering
Period, which election shall be made within such Offering Period and prior to
such First Purchase Date and shall be in writing on a form furnished by the
Company for such purpose and shall be made by having such Participant complete,
sign and file such form with the Company in the manner prescribed by the
Company.


(j)                                   “EMPLOYEE” means any person who receives a regular
stated compensation from the Company or a Subsidiary other than a pension,
severance pay, retainer, or fee under contract.


(k)                                “FAIR MARKET VALUE” of a Share of Common Stock on
a particular date shall be the average of the highest and lowest quoted selling
prices on such date (the “valuation date”) on the securities market where the
Common Stock of the Company is traded, or if there were no sales on the
valuation date, on the next preceding date within a reasonable period (as
determined in the sole discretion of the Committee) on which there were sales.
In the event that there were no sales in such a market within a reasonable
period, the fair market value shall be as determined in good faith by the
Committee in its sole discretion. The Fair Market Value as determined in this
paragraph shall be rounded down to the next lower whole cent if the foregoing
calculation results in fractional cents.



   
 









(l)                                   “OFFERING” means the offering of shares of Common
Stock to Participants pursuant to this Plan.


(m)                             “OFFERING DATE” means each May 15 and
November 15. If any such date shall fall other than on a business day, then
the Offering Date shall be the next succeeding business day.


(n)                               “OFFERING PERIOD” means either (i) the period
from an Offering Date through the second Purchase Date following such Offering
Date or (ii) if a Participant validly exercises an Election, the period
from an Offering Date through the first Purchase Date following such Offering
Date.


(o)                               “PARTICIPANT” means an Employee who has elected to
participate in the Plan.


(p)                               “PURCHASE DATE” means each May 14 and
November 14.


(q)                               “PLAN” means the Vertex Pharmaceuticals
Incorporated Employee Stock Purchase Plan, an “employee stock purchase plan”
within the meaning of Section 423(b) of the Code, together with any and
all amendments thereto.


(r)                                  “STOCK PURCHASE ACCOUNT,” with respect to a
Participant, means the account established on the books and records of the
Company or a Subsidiary for such Participant representing the payroll
deductions credited to such account in accordance with the provisions of the
Plan.


(s)                                “SUBSIDIARY” means any corporation, fifty percent
(50%) or more of the total combined voting power of all classes of stock of
which is beneficially owned, directly or indirectly, by the Company.


ARTICLE II


PARTICIPATION


 SECTION 2.1.  PARTICIPATION REQUIREMENTS.


(a)                                COMMENCEMENT OF PARTICIPATION.  Subject to Section 2.2 and
Section 3.2(b), each person who becomes an Employee after the Effective
Date may become a Participant in the Plan on any Offering Date following the
date on which such person becomes an Employee.


(b)                               ELIGIBILITY OF FORMER PARTICIPANTS.  If a person terminates employment with the
Company after becoming a Participant and subsequently resumes employment with
the Company, such person will again become eligible to participate on the
Offering Date next following such resumption of employment with the Company.


 SECTION 2.2.  EXCLUSIONS. 
Notwithstanding any provision of the Plan to the contrary, in no event
shall the following persons be eligible to participate in the Plan:


(a)                                Any Employee whose customary employment is twenty
(20) hours or less per week;


(b)                               Any Employee whose customary employment is for not
more than five (5) months in any calendar year; or


(c)                                Any Employee who, as of the beginning of an
Offering Period, owns (or under Section 423(b)(3) of the Code would be
deemed to own) stock possessing five percent (5%) or more of the total combined
voting power or value of all classes of stock of the Company or a Subsidiary.



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ARTICLE III


OFFERING OF
COMMON STOCK


 SECTION 3.1.  RESERVATION OF COMMON STOCK.  The Board of Directors shall reserve
1,748,660 shares of Common Stock for issuance under the Plan after
March 17, 2004, subject to adjustment in accordance with Section 3.4,
provided that no more than 248,660 of such shares shall be issued prior to
May 15, 2004.


 SECTION 3.2.  OFFERING OF COMMON STOCK.


(a)                                GENERAL. 
Subject to Section 3.2(b), each Participant in the Plan on an
Offering Date shall be entitled to purchase shares of Common Stock on each
Purchase Date within the Offering Period that begins with such Offering Date
with the amounts deducted from such Participant’s Compensation during such
Offering Period pursuant to Article IV, provided, however, that a
Participant shall not participate in more than one Offering Period
simultaneously. The purchase price for such shares of Common Stock shall be
determined under Section 3.3.


(b)                               LIMITATIONS. 
Notwithstanding Section 3.2(a), no employee may accrue rights to
purchase shares of Common Stock attributable to an Offering Period in excess of
$25,000 of fair market value of such shares (measured as of the relevant
Offering Date) for each calendar year during which such rights are outstanding.
For any year, this limit shall be further reduced by the fair market value of
stock (measured as of the relevant Offering Date for such stock) purchasable
under any prior outstanding rights relating to such calendar year under this
Plan and all other Code section 423 employee stock purchase plans of the
Company or any Subsidiary. This paragraph is intended to be consistent with the
limitation of Code section 423(b)(8) and shall be interpreted accordingly.


 SECTION 3.3.  DETERMINATION OF PURCHASE PRICE FOR OFFERED
COMMON STOCK.  The purchase price per
share of the shares of Common Stock to be acquired by a Participant on a
Purchase Date pursuant to an Offering shall be equal to eighty-five percent
(85%) of the lesser of:


(a)                                the Fair Market Value of a share of Common Stock
on the Offering Date for such Offering Period; or


(b)                               the Fair Market Value of a share of Common Stock
on such Purchase Date;


provided, however, in no event shall the purchase price
be less than the par value of a share of Common Stock.


 SECTION 3.4.  EFFECT OF CERTAIN TRANSACTIONS.  The number of shares of Common Stock reserved
for the Plan pursuant to Section 3.1, the maximum number of shares of
Common Stock offered pursuant to Section 3.2(b), and the determination
under Section 3.3 of the purchase price per share of the shares of Common
Stock offered to Participants pursuant to an Offering shall be appropriately
adjusted to reflect any increase or decrease in the number of issued shares of
Common Stock resulting from a stock split, a consolidation of shares, the
payment of a stock dividend, or any other capital adjustment affecting the
number of issued shares of Common Stock. In the event that the outstanding
shares of Common Stock shall be changed into or exchanged for a different
number or kind of shares of stock or other securities of the Company or another
corporation, whether through reorganization, recapitalization, merger, consolidation,
or otherwise, then there shall be substituted for each share of Common Stock
reserved for issuance under the Plan but not yet purchased by Participants, the
number and kind of shares of stock or other securities into which each
outstanding share of Common Stock shall be so changed or for which each such
share shall be exchanged.


ARTICLE IV


PAYROLL
DEDUCTIONS


 SECTION 4.1.  PAYROLL DEDUCTION ELECTIONS.  Any Employee eligible to participate in the
Plan may elect to have the Company deduct from the Compensation payable to such
Employee during each Offering Period any amount between one percent (1%) and
fifteen percent (15%) of such Participant’s Compensation, in whole multiples of
one percent (1%). Such election shall be made during the thirty day period
preceding the Offering Period to which it first relates. Such election shall
become effective as of the first day of such Participant’s first pay period
that begins on or after the first day of such Offering Period and shall remain 



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effective for each successive pay period and for each
subsequent Offering until changed or terminated pursuant to this
Article IV. The percentage deduction specified by the Participant will be
deducted from each payment of Compensation made to the Participant.


 SECTION 4.2.  ELECTION TO INCREASE OR DECREASE PAYROLL
DEDUCTIONS.  Subject to Section 4.4,
a Participant who has a payroll deduction election in effect under
Section 4.1 may prospectively increase or decrease during an Offering
Period the percentage amount of the deductions being made by the Company from
such Participant’s Compensation (including a decrease to zero) by delivering to
the Company written direction to make such change. Such change shall become
effective as soon as practicable after the Company’s receipt of such written
direction and shall remain in effect until changed or terminated pursuant to
this Article IV. A Participant shall be permitted to increase or decrease
the percentage amount of the deductions being made from such Participant’s
Compensation only once during each of the portions of an Offering Period that
ends on a Purchase Date; provided, however, a Participant may terminate the
deductions being made from such Participant’s Compensation at any time during
such Offering Period. If a Participant terminates deductions, such Participant
cannot resume deductions during that Offering Period.


 SECTION 4.3.  TERMINATION OF ELECTION UPON TERMINATION OF
EMPLOYMENT.  The termination of
employment of a Participant for any reason shall automatically terminate the
election of such Participant to have amounts deducted from such Participant’s
Compensation pursuant to this Article IV that is then in effect. Such
termination shall be effective immediately following the pay period during
which such termination of employment occurs, but shall not affect the deduction
from Compensation for that pay period.


 SECTION 4.4.  FORM OF ELECTIONS.  Except as otherwise permitted by the Company,
any election by a Participant regarding participation in or withdrawal from the
Plan or deductions from Compensation pursuant to this Article IV shall be
in writing on a form furnished by the Company for such purpose and shall be
made by having such Participant file such form with the Company in the manner
prescribed from time to time by the Company.


ARTICLE V


STOCK PURCHASE
ACCOUNTS AND PURCHASE OF COMMON STOCK


 SECTION 5.1.  STOCK PURCHASE ACCOUNTS.  A Stock Purchase Account shall be established
and maintained on the books and records of the Company for each Participant.
Amounts deducted from a Participant’s Compensation pursuant to Article IV
shall be credited to such Participant’s Stock Purchase Account. No interest or
other increment shall accrue or be payable to any Participant with respect to
any amounts credited to such Stock Purchase Accounts. All amounts credited to
such Stock Purchase Accounts shall be withdrawn, paid, or applied toward the
purchase of Common Stock pursuant to the provisions of this Article V.


 SECTION 5.2.  PURCHASE OF COMMON STOCK.


(a)                                GENERAL.  As
of each Purchase Date, the amount to the credit of a Participant in such
Participant’s Stock Purchase Account shall be used to purchase from the Company
on such Participant’s behalf the largest number of whole shares of Common Stock
which can be purchased at the price determined under Section 3.3 with the
amount then credited to such Participant’s Stock Purchase Account, subject to
the limitations set forth in Article III on the maximum number of shares
of Common Stock such Participant may purchase. As of such date, such
Participant’s Stock Purchase Account shall be charged with the aggregate
purchase price of the shares of Common Stock purchased on such Participant’s
behalf. No brokerage or other fees are to be charged upon a purchase. Stock
transfer taxes, if any, shall be paid by the Company. The remaining balance, if
any, credited to such Participant’s Stock Purchase Account shall be carried
forward and used to purchase shares of Common Stock on the next succeeding
Purchase Date; provided that any excess balance remaining in a Participant’s
Stock Purchase Account after the application of the limitations in
Section 3.2 shall be refunded to the Participant.


(b)                               ISSUANCE OF COMMON STOCK.  The shares of Common Stock purchased for a
Participant as of a Purchase Date shall be deemed to have been issued by the
Company for all purposes as of the close of business on such date. Prior to
such date, none of the rights and privileges of a stockholder of the Company
shall exist with respect to such shares of Common Stock. As soon as practicable
after such a Purchase Date the Company shall issue and deliver, or shall cause
its stock transfer agent to issue and deliver, a certificate for the number of
shares of Common Stock purchased for a Participant, which certificate shall be
issued in the Participant’s name or, if so specified by the Participant, in the
name of the Participant and such other person as the Participant shall 



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designate as joint tenants with right of survivorship. In lieu of
issuing a certificate, the Company may elect to deliver to the Participant a
statement which shall indicate the number of shares of Common Stock purchased
for such Participant and the aggregate number of shares of Common Stock held on
behalf of such Participant under the Plan.


(c)                                INSUFFICIENT COMMON STOCK AVAILABLE.  If, as of any Purchase Date, the aggregate
Stock Purchase Accounts available for the purchase of shares of Common Stock
pursuant to Section 5.2(a) would purchase a number of shares of Common
Stock in excess of the number of shares of Common Stock then available for
purchase under the Plan, (i) the number of shares of Common Stock which
would otherwise be purchased for each Participant on such date shall be reduced
proportionately to the extent necessary to eliminate such excess, (ii) the
remaining balance to the credit of each Participant in each such Participant’s
Stock Purchase Accounts shall be distributed to each such Participant, and
(iii) the Plan shall terminate automatically upon the distribution of the
remaining balance in such Stock Purchase Accounts.


 SECTION 5.3.  WITHDRAWAL FROM PLAN PRIOR TO PURCHASE OF
COMMON STOCK.  In the event (i) a
Participant elects in writing for any reason to withdraw from the Plan during
an Offering Period or (ii) a Participant’s employment with the Company
terminates for any reason prior to the end of an Offering Period, then the
entire amount remaining to the credit of such Participant in such Participant’s
Stock Purchase Account shall be distributed to such Participant (or, if such
Participant is deceased, to such Participant’s Beneficiary) as soon as
administratively practicable after such withdrawal or termination of employment
(as the case may be).


ARTICLE VI


COMMITTEE


 SECTION 6.1.  POWERS OF THE COMMITTEE.  The Committee shall administer the Plan. The
Committee shall have all powers necessary to enable it to carry out its duties
under the Plan properly. Not in limitation of the foregoing, the Committee
shall have the power to construe and interpret the Plan and to determine all
questions that shall arise thereunder. The decision of the Committee upon all
matters within the scope of its authority shall be final and conclusive on all
persons, except to the extent otherwise provided by law.


 SECTION 6.2.  INDEMNIFICATION OF THE COMMITTEE.  The Company agrees to indemnify and hold
harmless the members of the Committee against any liabilities, loss, costs, or
damage that they may incur in acting as such members and to assume the defense
of any and allocations, suits, or proceedings against the members of the
Committee, to the extent permitted by applicable law.


ARTICLE VII


AMENDMENT AND
TERMINATION


 SECTION 7.1.  AMENDMENT OF THE PLAN.  The Company expressly reserves the right, at
any time and from time to time, to amend in whole or in part any of the terms
and provisions of the Plan; provided, however, no amendment may without the
approval of the shareholders of the Company increase the number of shares of
Common Stock reserved under the Plan.


 SECTION 7.2.  TERMINATION OF PLAN.  The Company expressly reserves the right, at
any time and for whatever reason it may deem appropriate, to terminate the
Plan. The Plan shall continue in effect until terminated pursuant to (i) 
the preceding sentence or (ii)  Section 5.2(c). Upon any termination
of the Plan, the entire amount credited to the Stock Purchase Account of each
Participant shall be distributed to each such Participant.


 SECTION 7.3.  PROCEDURE FOR AMENDMENT OR TERMINATION.  Any amendment to the Plan or termination of
the Plan may be retroactive to the extent not prohibited by applicable law. Any
amendment to the Plan or termination of the Plan shall be made by the Company
by resolution of the Board of Directors (subject to Section 7.1) and shall
not require the approval or consent of any Participant or Beneficiary in order
to be effective.



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ARTICLE VIII


MISCELLANEOUS


 SECTION 8.1.  ADOPTION BY A SUBSIDIARY.  A Subsidiary may, with the approval of the
Board of Directors and the board of directors of such Subsidiary, elect to
adopt the Plan as of a date mutually agreeable to the Board of Directors and
the board of directors of such Subsidiary. Any such adoption of the Plan by a
Subsidiary shall be evidenced by an appropriate instrument of adoption executed
by such Subsidiary.


 SECTION 8.2.  AUTHORIZATION AND DELEGATION TO THE BOARD OF
DIRECTORS.  Each Subsidiary that
hereafter adopts the Plan authorizes the Board of Directors (i) to amend
or terminate the Plan without further action by said Subsidiary as provided in
Article VII and (ii) to perform such other acts and to do such other
things as the Board of Directors is expressly directed, authorized, or
permitted to perform or do as provided herein.


 SECTION 8.3.  TRANSFERABILITY OF RIGHTS.  Rights under the Plan are not transferable by
a Participant other than by will or the laws of descent and distribution and
are exercisable during a Participant’s lifetime only by the Participant.


 SECTION 8.4.  NO EMPLOYMENT RIGHTS.  Participation in the Plan shall not give any
employee of the Company or any Subsidiary any right to remain employed or, upon
termination of employment, any right or interest in the Plan, except as
expressly provided herein.


 SECTION 8.5.  COMPLIANCE WITH LAW.  No shares of Common Stock shall be issued
under the Plan prior to compliance by the Company to the satisfaction of its
counsel with any applicable laws.


 SECTION 8.6.  CONSTRUCTION. 
Article, Section, and paragraph headings have been inserted in the Plan
for convenience of reference only and are to be ignored in any construction of
the provisions hereof. If any provision of the Plan shall be invalid or
unenforceable, the remaining provisions shall nevertheless be valid,
enforceable, and fully effective. It is the intent that the Plan shall at all
times constitute an “employee stock purchase plan” within the meaning of
Section 423(b) of the Code, and the Plan shall be construed, and
interpreted to remain such. The Plan shall be construed, administered,
regulated, and governed by the laws of the United States to the extent
applicable, and to the extent such laws are not applicable, by the laws of The
Commonwealth of Massachusetts. Without limiting the foregoing, all Participants
for an Offering Period shall have the same rights and privileges with respect
to their rights to acquire Common Stock under the Plan for such period, subject
to the express terms hereof.



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