Exhibit 10.44
SEPARATION AGREEMENT & GENERAL RELEASE

THIS SEPARATION AGREEMENT & GENERAL RELEASE (“Agreement”) is made and entered
into by and between DAVID T. “TY” HOWTON (“Employee”) and VERTEX PHARMACEUTICALS
INCORPORATED (the “Company”) as of the Effective Date (as such term is defined
in Section 12 below).
WHEREAS, Employee and the Company executed an Employment Agreement dated the
26th day of January, 2012 (the “Employment Agreement”).
WHEREAS, Employee is entitled to a Severance Payment and other post-employment
benefits if he signs a general release of all claims against the Company, its
subsidiaries, and their officers, directors, agents and representatives.
WHEREAS, the Company wishes to provide Employee with certain additional
transition pay in exchange for Employee signing and returning this Agreement as
provided in Section 12 below.
NOW, THEREFORE, in consideration of the mutual promises, representations,
warranties and covenants contained herein and other good and valuable
consideration to which Employee agrees Employee is not otherwise entitled, it is
hereby agreed by and between the parties hereto as follows:
1.SEPARATION OF EMPLOYMENT & TRANSITION PAY. Employee is hereby notified that
his employment has been terminated by the Company without cause, effective as of
Friday, November 2, 2012 (the “Separation Date”), and Employee shall thereafter
cease to be an employee or officer of the Company for all purposes. In
accordance with Employee’s Employment Agreement, if Employee signs this
Agreement and it becomes effective as set forth in Section 12 below, in exchange
for the general release and the other terms set forth herein, the Company will
provide Employee with:
(a)    a severance payment of $412,000.12;
(b)    a payment of $144,200.04 representing Employee’s target bonus for 2012;
and
(c)    a supplemental transition payment of $305,000.00.
The payments set forth in this Section 1 shall be subject to voluntarily
authorized and legally required payroll deductions and withholdings, and shall
be payable in a lump sum on or before the Company’s first regular pay date
immediately following the Effective Date of this Agreement.
2.    MEDICAL INSURANCE. To the extent permitted by the federal COBRA law and by
the Company’s current group medical insurance policies, and provided that COBRA
is properly elected, Employee will be eligible for continued participation in
the Company’s group medical insurance plan(s), to the extent that such coverage
is extended to current employees of the Company. If Employee signs this
Agreement and it becomes effective as set forth in Section 12 below, and if
Employee properly elects continued participation in the Company’s group medical
insurance plan(s), the Company will pay the entire premium for such coverage
until the earlier of: (a) the date twelve (12) months following the Separation
Date, or (b) the date, or dates, on which Employee receives equivalent coverage
and benefits under the plans, programs and/or arrangements of a subsequent
employer. At the end of the applicable period, and pursuant to the provisions of
COBRA, Employee will have the right to continue Employee’s participation, at

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Employee’s own cost. The Company’s payment of the premium does not extend the
length of the COBRA continuation period. A notice of Employee’s COBRA rights
will be provided under separate cover.
3.    ACCRUED SALARY & PAID VACATION. On the Separation Date, the Company will
pay Employee all accrued salary and all accrued and unused vacation, less
standard applicable payroll deductions and withholdings. Employee is entitled to
these payments irrespective of whether Employee signs this Agreement. If
Employee has taken days of vacation not yet earned, then the dollar value of
that vacation will be deducted from Employee’s transition pay. If the transition
pay does not exceed the value of the unearned vacation, or if this Agreement
does not become a binding legal agreement between the parties, Employee will be
required to reimburse the Company for the unearned vacation in accordance with
applicable law.
4.    EQUITY. Employee’s equity granted pursuant to the Company’s 1996 and 2006
Stock & Option Plan (the “Stock Plan”) will vest in accordance with the
appropriate stock plan and Employee’s equity agreement with the Company. The
Company will provide Employee with a summary of Employee’s equity information
under separate cover.
5.    OTHER BENEFITS OR COMPENSATION. The terms of this agreement shall not
modify the terms of the “Amended & Restated Change of Control Agreement” dated
January 26, 2012, previously entered into by and between Employee and the
Company. Employee’s participation in all Company benefit plans will terminate as
of the Separation Date, except as expressly provided herein. Employee represents
and warrants that Employee has received all leave (paid or unpaid),
compensation, wages, bonuses, commissions, and/or benefits to which Employee may
be entitled and that no other leave (paid or unpaid), compensation, wages,
bonuses, commissions and/or benefits are due to Employee, except as provided in
this Agreement. Employee also affirms that Employee has no known workplace
injuries or occupational diseases. The benefits provided hereunder are not
intended to and do not constitute a severance plan.
6.    RETURN OF COMPANY PROPERTY; EXPENSE REIMBURSEMENT. Employee represents
that on or before the Separation Date, all Company documents (and all copies
thereof) and other Company property and materials in Employee’s possession or
control, including, but not limited to, Company files, notes, memoranda,
correspondence, lists, drawings, records, plans and forecasts, computer-recorded
information, tangible property, equipment, credit cards, entry cards,
identification badges and keys, and any materials of any kind which contain or
embody any proprietary or confidential information of the Company (and all
reproductions thereof) have been returned to the Company. Employee further
represents that on or before the Separation Date, Employee has submitted a final
documented expense reimbursement statement reflecting all business expenses
Employee incurred through the Separation Date, if any, for which Employee seeks
reimbursement. Employee will not be entitled to reimbursement for any expenses
incurred by Employee after the Separation Date.
7.    PROPRIETARY INFORMATION OBLIGATIONS. Nothing herein shall impair
Employee’s covenants and obligations set forth in the “Employee Non-Disclosure,
Non-Competition & Inventions Agreement” (the “Inventions Agreement”) previously
executed by Employee, a copy of which is attached hereto as Exhibit A and is
incorporated herein by reference, and Employee shall otherwise abide by all
common law and/or statutory obligations relating to protection and
non-disclosure of Company’s trade secrets and/or confidential and proprietary
documents and information.
8.    CONFIDENTIALITY. The provisions of this Agreement shall be held by
Employee in strictest confidence, and shall not be publicized or disclosed in
any manner whatsoever; provided, however, that Employee may disclose this
Agreement, in confidence, to: (a) Employee’s immediate family; (b) Employee’s

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attorneys, accountants, auditors, tax preparers, and financial advisors; and (c)
as required in connection with legal process or in response to a valid request
for information by a regulatory body.
9.    COOPERATION. Employee shall provide the Company with assistance regarding
any claim or dispute, whether threatened or actual, against the Company by any
third party arising out of services provided by Employee, in any capacity,
during his employment at the Company, which assistance shall include, but not be
limited to, providing consultation, responding to interrogatories, appearing at
depositions and testifying in any investigation, settlement proceeding or
litigation proceeding. Under no circumstances shall Employee charge the Company
or any insurer of the Company for such assistance, provided that the Company
shall reimburse Employee for all reasonable out-of-pocket expenses, including
travel expenses, incurred by Employee when providing such assistance. Such
out-of-pocket expenses do not include attorneys’ fees, should Employee retain
separate counsel.
10.    NON-DISPARAGEMENT. Employee shall not make or publish, directly or
indirectly, any oral or written statements or comments with respect to the
Company, its parents, affiliates and subsidiaries, and their officers,
directors, agents, employees, attorneys, shareholders, successors and assigns
that are critical, derogatory, or which may tend to injure their business or
reputation.
11.    EMPLOYEE’S RELEASE OF CLAIMS. Employee hereby releases, acquits and
forever discharges the Company, its parents and subsidiaries, and their
officers, directors, agents, servants, employees, attorneys, shareholders,
successors, assigns and affiliates (collectively, the “Releasees”), of and from
any and all claims, liabilities, demands, causes of action, costs, expenses,
attorneys fees, damages, indemnities and obligations of every kind and nature,
in law, equity, or otherwise, known and unknown, suspected and unsuspected,
disclosed and undisclosed, arising out of or in any way related to agreements,
events, acts or conduct at any time prior to and including the execution date of
this Agreement, including but not limited to: all such claims and demands
directly or indirectly arising out of or in any way connected with Employee’s
employment with the Company or the termination of that employment; all claims or
demands related to salary, bonuses, commissions, stock, stock options, or any
other ownership interests in the Company, vacation pay, fringe benefits, expense
reimbursements, severance pay, or any other form of compensation; all claims
pursuant to any federal, state or local law, statute or cause of action
including, but not limited to, the Age Discrimination in Employment Act, as
amended; the Civil Rights Act of 1964, as amended; the Americans With
Disabilities Act of 1990; the Worker Adjustment and Retraining Notification Act
of 1988, as amended; the Employee Retirement Income Security Act of 1974, as
amended; the Family and Medical Leave Act of 1993, as amended; the Massachusetts
Fair Employment Practices Act, Civil Rights Act, Equal Pay Act, Maternity Leave
Act, Privacy Statute, Consumer Protection Act, and labor code; tort law;
contract law; wrongful discharge; discrimination; harassment; fraud; defamation;
emotional distress; and breach of the implied covenant of good faith and fair
dealing; and all claims that might be made by any other person or organization
on Employee’s behalf (and Employee specifically waives any right to recover
damage awards in any case in which a claim is made by another person or
organization on Employee’s behalf). Notwithstanding the foregoing, nothing in
this Agreement shall bar or prohibit Employee from contacting, seeking
assistance from or participating in any proceeding before any federal or state
administrative agency to the extent permitted by applicable federal, state
and/or local law (but Employee acknowledges that Employee may not be able to
recover any monetary benefits in connection with any such participation or
proceeding), nor shall anything in this paragraph bar or prohibit Employee from
enforcing Employee’s rights or the Company’s obligations under this Agreement.
This Agreement is not intended to, and does not govern, any claims that cannot
be release by private agreement.
12.    ADEA WAIVER; EFFECTIVE DATE OF AGREEMENT. Employee acknowledges that
Employee knowingly and voluntarily waives and releases any rights Employee may
have under the Age

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Discrimination in Employment Act, as amended (“ADEA”). Employee acknowledges
that the consideration given for the release in this Agreement is in addition to
anything of value to which Employee was already entitled. Employee further
acknowledges that Employee has been advised by this writing that: (a) Employee’s
waiver and release do not apply to any rights or claims that may arise after the
execution date of this Agreement; (b) Employee should consult with an attorney
prior to executing this Agreement; (c) Employee has twenty-one (21) days from
the date that Employee receives this Agreement to accept the terms of this
Agreement (although Employee may choose to voluntarily execute this Agreement
earlier) by signing below and returning it to Vertex Pharmaceuticals
Incorporated, c/o Lisa Kelly-Croswell, Sr. Vice President, Human Resources, 130
Waverly Street, Cambridge, MA 02139; (d) if Employee thereafter desires to
revoke acceptance of this Agreement, Employee must do so by notice to Lisa
Kelly-Croswell within seven (7) days following the execution of this Agreement;
and (e) this Agreement shall not be effective until the date upon which the
revocation period has expired, which shall be the eighth day after this
Agreement is executed by Employee, and Employee has not revoked Employee’s
acceptance of this Agreement (the “Effective Date”). The parties agree that any
changes to the offer in this Agreement, whether material or not, do not restart
the running of the 21-day period. This Section applies to the extent permitted
by law and, in the event any claim or charge is permitted by law, Employee
expressly waives Employee’s right to receive any relief, recovery and/or damages
as a result of any such charge or claim.
13.    COVENANTS. Employee’s breach of any of the covenants set forth in this
Agreement shall constitute a material breach of this Agreement and shall relieve
the Company of any further obligations hereunder. In addition to any other legal
or equitable remedy available to the Company, the Company shall be entitled to
recover any monies paid to or on behalf of Employee pursuant to this Agreement
and shall be entitled to enforce the terms of the non-compete provisions under
the Inventions Agreement.
14.    ENTIRE AGREEMENT; REPRESENTATIONS. This Agreement and all documents
incorporated herein by reference, including all exhibits, constitute the
complete, final and exclusive embodiment of the entire agreement between
Employee and Company with regard to the subject matter hereof. It supersedes any
and all agreements entered into by and between Employee and Company where such
other agreement may conflict with this Agreement. It is entered into without
reliance on any promise or representation, written or oral, other than those
expressly contained herein. It may not be modified except in a writing signed by
Employee and a duly authorized officer of the Company. Employee represents that
Employee has carefully read this Agreement, has been afforded the opportunity to
be advised of its meaning and consequences by Employee’s attorney, and has
signed the same of Employee’s own free will.
15.    NO LIABILITY OR WRONGDOING. The parties hereto agree and acknowledge that
this Agreement is intended only to settle all matters between the parties and
nothing contained in this Agreement, nor any of its terms and provisions, nor
any of the negotiations or proceedings connected with it, constitutes, will be
construed to constitute, will be offered in evidence as, received in evidence as
and/or deemed to be evidence of an admission of liability or wrongdoing by any
and/or all of the Releasees, and any such liability or wrongdoing is hereby
expressly denied by each of the Releasees.
16.    MISCELLANEOUS. This Agreement shall bind the heirs, personal
representatives, successors, assigns, executors and administrators of each
party, and inure to the benefit of each party, its heirs, successors and
assigns. This Agreement shall be deemed to have been entered into and shall be
construed and enforced in accordance with the laws of the Commonwealth of
Massachusetts as applied to contracts made and to be performed entirely within
Massachusetts. If a court of competent jurisdiction determines that any term or
provision of this Agreement is invalid or unenforceable, in whole or in part,
then the remaining terms and provisions hereof shall be unimpaired, the invalid
or unenforceable term or provision shall be modified or replaced so as to render
it valid and enforceable in a manner which represents the parties’ intention
with

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respect to the invalid or unenforceable term or provision insofar as possible.
This Agreement may not be modified, altered or changed except upon express
written consent of all parties wherein specific reference is made to this
Agreement. This Agreement may be executed in two counterparts, each of which
shall be deemed an original, all of which together shall constitute one and the
same instrument.

[SIGNATURE PAGE TO FOLLOW]

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SEPARATION AGREEMENT & GENERAL RELEASE

[SIGNATURE PAGE]

IN WITNESS WHEREOF, the parties have duly authorized and caused this Agreement
to be executed as follows:

VERTEX PHARMACEUTICALS INCORPORATED

By: /s/ Lisa Kelly-Croswell    

Name: Lisa Kelly-Croswell    

Title: Sr. Vice President, Human Resources    

Date: _11/29/2012_____________________

EMPLOYEE ACKNOWLEDGES AND AGREES THAT EMPLOYEE HAS TWENTY-ONE (21) CALENDAR DAYS
TO REVIEW THIS AGREEMENT AND GENERAL RELEASE, AND IS HEREBY ADVISED TO CONSULT
WITH AN ATTORNEY PRIOR TO EXECUTION OF THIS AGREEMENT AND GENERAL RELEASE.

EMPLOYEE FURTHER ACKNOWLEDGES AND AGREES THAT EMPLOYEE HAS CAREFULLY READ THIS
AGREEMENT AND GENERAL RELEASE IN ITS ENTIRETY, FULLY UNDERSTANDS THE
SIGNIFICANCE OF ALL OF ITS TERMS AND PROVISIONS, AND AGREES TO FULFILL THE
PROMISES AND RECEIVE THE CONSIDERATION ABOVE.

ACCORDINGLY, EMPLOYEE ACKNOWLEDGES AND AGREES THAT EMPLOYEE IS EXECUTING THIS
AGREEMENT AND GENERAL RELEASE FREELY, KNOWINGLY AND VOLUNTARILY, AND AFTER DUE
CONSIDERATION, INTENDING TO WAIVE, SETTLE AND RELEASE ALL CLAIMS EMPLOYEE HAS OR
MIGHT HAVE AGAINST THE RELEASEES, INCLUDING ANY AND ALL CLAIMS UNDER THE AGE
DISCRIMINATION IN EMPLOYMENT ACT.

EMPLOYEE

/s/ David T. Howton    

Date: 11/29/2012______________________

Date Separation Agreement & General Release Delivered to Employee: November 7,
2012

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