Document:

EX-10.1

LIONBRIDGE TECHNOLOGIES, INC.

2005 STOCK INCENTIVE PLAN

As amended and restated on May 1, 2009

1. Purpose

The purpose of this 2005 Stock Incentive Plan (the “Plan”) of Lionbridge Technologies, Inc., a
Delaware corporation (the “Company”), is to advance the interests of the Company’s stockholders by
enhancing the Company’s ability to attract, retain and motivate persons who are expected to make
important contributions to the Company and by providing such persons with equity ownership
opportunities and performance-based incentives that are intended to align their interests with
those of the Company’s stockholders. Except where the context otherwise requires, the term
“Company” shall include any of the Company’s present or future parent or subsidiary corporations as
defined in Sections 424(e) or (f) of the Internal Revenue Code of 1986, as amended, and any
regulations promulgated thereunder (the “Code”) and any other business venture (including, without
limitation, joint venture or limited liability company) in which the Company has a controlling
interest, as determined by the Board of Directors of the Company (the “Board”).

2. Eligibility

All of the Company’s employees, officers, directors, consultants and advisors are eligible to
receive options, stock appreciation rights, restricted stock, restricted stock units and other
stock-based awards (each, an “Award”) under the Plan. Each person who receives an Award under the
Plan is deemed a “Participant”.

3. Administration and Delegation

(a) Plan Administration and Discretionary Authority.

(1) The Plan will be administered by the Nominating and Compensation Committee of the Board or
such other committee of the Board as may be designated by the Board to administer the Plan (a
“Committee”), which committee shall consist of two or more members of the Board, each of whom is
both a “non-employee director” within the meaning of Rule 16b-3 promulgated under the Exchange Act
and an “outside director” within the meaning of such term as contained in applicable regulations
interpreting section 162(m) of the Code; provided, however, that with respect to the application of
the Plan to Awards made to non-employee director of the Company, the term “Committee” means the
Board. To the extent that no Committee exists that has the authority to administer the Plan, the
functions of the Committee shall be exercised by the Board. If for any reason the appointed
Committee does not meet the requirements of Rule 16b-3 or section 162(m) of the Code, such
noncompliance with such requirements shall not affect the validity of Awards, grants,
interpretations or other actions of the Committee.

(2) The Committee shall have authority to grant Awards and to adopt, amend and repeal such
administrative rules, guidelines and practices relating to the Plan as it shall deem advisable.
Without limiting the generality of the preceding sentence, the Committee shall have the exclusive
right to: (i) interpret the Plan and the Award Agreements executed hereunder; (ii) decide all
questions concerning eligibility for, and the amount of, Awards granted under the Plan; (iii)
construe any ambiguous provision of the Plan or any Award Agreement; (iv) prescribe the form of
Award Agreements; (v) correct any defect, supply any omission or reconcile any inconsistency in the
Plan or any Award Agreement; (vi) issue administrative guidelines as an aid to administering the
Plan and make changes in such guidelines as the Committee from time to time deems proper; (vii)
make regulations for carrying out the Plan and make changes in such regulations as the Committee
from time to time deems proper; (viii) determine whether Awards should be granted singly or in
combination; (ix) to the extent permitted under the Plan, grant waivers of Plan terms, conditions,
restrictions and limitations; (x) subject to the terms of the Plan, accelerate the exercise,
vesting or payment of an Award when such action or actions would be in the best interests of the
Company; (xi) require Participants to hold a stated number or percentage of shares of Common Stock
acquired pursuant to an Award for a stated period; and (xii) take any and all other actions the
Committee deems necessary or advisable for the proper operation or administration of the Plan. The
Committee shall have authority in its sole discretion with respect to all matters related to the
discharge of its responsibilities and the exercise of its authority under the Plan, including
without limitation its construction of the terms of the Plan and its determination of eligibility
for participation in, and the terms of Awards granted under, the Plan. The decisions of the
Committee and its actions with respect to the Plan shall be final, conclusive and binding on all
persons having or claiming to have any right or interest in or under the Plan, including without
limitation Participants and their respective permitted transferees, estates, beneficiaries and
legal representatives. No director or person acting pursuant to the authority delegated by the
Committee shall be liable for any action or determination relating to or under the Plan made in
good faith. In the case of an Award intended to be eligible for the performance-based compensation
exemption under section 162(m) of the Code, the Committee shall exercise its discretion consistent
with qualifying the Award for such exemption.

(b) Delegation. To the extent permitted by applicable law, the Committee may delegate
to one or more directors and/or officers of the Company the power to grant Awards to employees or
officers of the Company or any of its present or future subsidiary corporations and to exercise
such other powers under the Plan as the Committee may determine, provided that the Committee shall
fix the terms of the Awards to be granted by such officers (including the exercise price of such
Awards, which may include a formula by which the exercise price will be determined) and the maximum
number of shares subject to Awards that the officers may grant; provided further, however, that no
officer shall be authorized to grant Awards to any “executive officer” of the Company (as defined
by Rule 3b-7 under the Securities Exchange Act of 1934, as amended (the “Exchange Act”)) or to any
“officer” of the Company (as defined by Rule 16a-1 under the Exchange Act).

4. Stock Available for Awards

(a) Number of Shares. Subject to adjustment under Section 10, Awards may be made
under the Plan for up to 8,500,000 shares of common stock, $0.01 par value per share, of the
Company (the “Common Stock”). If any Award expires or is terminated, surrendered or canceled
without having been fully exercised or is forfeited in whole or in part (including as the result of
shares of Common Stock subject to such Award being repurchased by the Company at the original
issuance price pursuant to a contractual repurchase right) or results in any Common Stock not being
issued, the unused Common Stock covered by such Award shall again be available for the grant of
Awards under the Plan. For purposes of counting the number of shares available for the grant of
Awards under the Plan, (i) shares of Common Stock covered by independent SARs shall be counted
against the number of shares available for the grant of Awards under the Plan; provided, however,
that independent SARs that may be settled in cash only shall not be so counted; (ii) if any Award
(A) expires or is terminated, surrendered or canceled without having been fully exercised or is
forfeited in whole or in part (including as the result of shares of Common Stock subject to such
Award being repurchased by the Company at the original issuance price pursuant to a contractual
repurchase right) or (B) results in any Common Stock not being issued (including as a result of an
independent SAR that was settleable either in cash or in stock actually being settled in cash), the
unused Common Stock covered by such Award shall again be available for the grant of Awards under
the Plan; provided, however, in the case of Incentive Stock Options (as hereinafter defined), the
foregoing shall be subject to any limitations under the Code; and (iii) shares of Common Stock
tendered to the Company by a Participant to (A) purchase shares of Common Stock upon the exercise
of an Award or (B) satisfy tax withholding obligations (including shares retained from the Award
creating the tax obligation) shall not be added back to the number of shares available for the
future grant of Awards under the Plan. However, in the case of Incentive Stock Options (as
hereinafter defined), the foregoing provisions shall be subject to any limitations under the Code.
Shares issued under the Plan may consist in whole or in part of authorized but unissued shares or
treasury shares.

(b) Sub-limits. Subject to adjustment under Section 10, the following sub-limits on
the number of shares subject to Awards shall apply:

Section 162(m) Per-Participant Limit. The maximum number of shares of Common Stock with
respect to which Awards may be granted to any Participant under the Plan shall be 600,000 per
calendar year and the maximum number of shares of Common Stock that may be subject to Awards other
than Options and SARs granted under the Plan to any one Participant per calendar year is 300,000.
The maximum number of shares of Common Stock that may be subject to a Performance Award that
provides for a performance period longer than one calendar year shall be based upon the foregoing
annual maximum limits multiplied by the number of full calendar years in the performance period.
For purposes of the foregoing limit, the combination of an Option in tandem with an SAR (as each is
hereafter defined) shall be treated as a single Award. The per-Participant limit described in this
Section 4(b)(1) shall be construed and applied consistently with Section 162(m) of the Code or any
successor provision thereto, and the regulations thereunder (“Section 162(m)”).

5. Stock Options

(a) General. The Committee may grant options to purchase Common Stock (each, an
“Option”) and determine the number of shares of Common Stock to be covered by each Option, the
exercise price of each Option and the conditions and limitations applicable to the exercise of each
Option, including conditions relating to applicable federal or state securities laws, as it
considers necessary or advisable. An Option which is not intended to be an Incentive Stock Option
(as hereinafter defined) shall be designated a “Nonstatutory Stock Option”.

(b) Incentive Stock Options. An Option that the Committee intends to be an “incentive
stock option” as defined in Section 422 of the Code (an “Incentive Stock Option”) shall only be
granted to employees of Lionbridge Technologies, Inc., any of Lionbridge Technologies, Inc.’s
present or future parent or subsidiary corporations as defined in Sections 424(e) or (f) of the
Code, and any other entities the employees of which are eligible to receive Incentive Stock Options
under the Code, and shall be subject to and shall be construed consistently with the requirements
of Section 422 of the Code. The Company shall have no liability to a Participant, or any other
party, if an Option (or any part thereof) that is intended to be an Incentive Stock Option is not
an Incentive Stock Option or for any action taken by the Committee pursuant to Section 11(f),
including without limitation the conversion of an Incentive Stock Option to a Nonstatutory Stock
Option.

(c) Exercise Price. The Committee shall establish the exercise price of each Option
and specify such exercise price in the applicable option agreement provided, however, that the
exercise price of such Option shall not be less than 100% than the fair market value of the Common
Stock on the date of grant.

(d) Duration of Options. Each Option shall be exercisable at such times and subject
to such terms and conditions as the Committee may specify in the applicable option agreement.
However, no option will remain exercisable for a period greater than ten years from the date of
grant and no option will become exercisable in whole or in part in less than one year unless:

(1) the Option was granted as an inducement to an individual becoming an employee of the
Company or in connection with the individual’s promotion to a more senior position within the
Company (as determined in the discretion of the Committee); provided, however that no more than
7.5% of the total number of shares authorized under the Plan may be so issued in the aggregate
during the term of the Plan; or

(2) the Option was granted in lieu of a previously earned cash award.

(e) Exercise of Option. Options may be exercised by delivery to the Company of a
written notice of exercise signed by the proper person or by any other form of notice (including
electronic notice) approved by the Committee together with payment in full as specified in Section
5(f) for the number of shares for which the Option is exercised. Shares of Common Stock subject to
the Option will be delivered by the Company following exercise either as soon as practicable or,
subject to such conditions as the Committee shall specify, on a deferred basis (with the Company’s
obligation to be evidenced by an instrument providing for future delivery of the deferred shares at
the time or times specified by the Committee).

(f) Payment Upon Exercise. Common Stock purchased upon the exercise of an Option
granted under the Plan shall be paid for as follows:

(1) in cash or by check, payable to the order of the Company;

(2) except as the Board may otherwise provide in an option agreement, by (i) delivery of an
irrevocable and unconditional undertaking by a creditworthy broker to deliver promptly to the
Company sufficient funds to pay the exercise price and any required tax withholding or (ii)
delivery by the Participant to the Company of a copy of irrevocable and unconditional instructions
to a creditworthy broker to deliver promptly to the Company cash or a check sufficient to pay the
exercise price and any required tax withholding;

(3) when the Common Stock is registered under the Securities Exchange Act of 1934 (the
“Exchange Act”), by delivery of shares of Common Stock owned by the Participant valued at their
fair market value as determined by (or in a manner approved by) the Committee (“Fair Market
Value”), provided (i) such method of payment is then permitted under applicable law, (ii) such
Common Stock, if acquired directly from the Company, was owned by the Participant for such minimum
period of time, if any, as may be established by the Committee in its discretion and (iii) such
Common Stock is not subject to any repurchase, forfeiture, unfulfilled vesting or other similar
requirements;

(4) to the extent permitted by applicable law including, without limitation, Section 402 of
the Sarbanes-Oxley Act and the rules thereunder, and by the Board, by (i) delivery of a promissory
note of the Participant to the Company on terms determined by the Committee, or (ii) payment of
such other lawful consideration as the Board may determine; or

(5) by any combination of the above permitted forms of payment.

(g) Substitute Options. In connection with a merger or consolidation of an entity
with the Company or the acquisition by the Company of property or stock of an entity, the Committee
may grant Options in substitution for any options or other stock or stock-based awards granted by
such entity or an affiliate thereof. Substitute Options may be granted on such terms as the
Committee deems appropriate in the circumstances, notwithstanding any limitations on Options
contained in the other sections of this Section 5 or in Section 2. Substitute Options shall not
count against the overall share limit set forth in Section 4(a), except as may be required by
reason of Section 422 and related provisions of the Code.

(h) No Reload Rights. No Option granted under the Plan shall contain any provision
entitling the optionee to the automatic grant of additional Options in connection with any exercise
of the original Option.

(i) Limitation on Repricing. Unless such action is approved by the Company’s
stockholders: (1) no outstanding Option granted under the Plan may be amended to provide an
exercise price per share that is lower than the then-current exercise price per share of
such outstanding Option (other than adjustments pursuant to Section 10) and (2) the
Committee may not cancel any outstanding option (whether or not granted under the Plan) and
grant in substitution therefore new Awards under the Plan covering the same or a different
number of shares of Common Stock and having an exercise price per share lower than the
then-current exercise price per share of the cancelled option.

6. Director Awards.

(a) Initial Grant. Upon the commencement of service on the Board by any individual
who is not then an employee of the Company or any subsidiary of the Company, and who does not
beneficially hold, directly or indirectly, more than 1% of the outstanding shares of the Company’s
equity securities, the Company shall grant to such person a Nonstatutory Stock Option to purchase
20,000 shares of Common Stock (subject to adjustment under Section 10).

(b) Annual Grant. On the date of each annual meeting of stockholders of the Company
(or on June 30 of any calendar year, if the annual meeting of stockholders has not occurred by such
date), the Company shall grant to each member of the Board of Directors of the Company who is both
serving as a director of the Company immediately prior to and immediately following such annual
meeting and who is not then an employee of the Company or any of its subsidiaries and who does not
beneficially hold, directly or indirectly, more than 1% of the outstanding shares of the Company’s
equity securities, a Nonstatutory Stock Option to purchase 10,000 shares of Common Stock (subject
to adjustment under Section 10); provided, however, that a director shall not be eligible to
receive an option grant under this Section 6(b) until such director has served on the Board for at
least six months.

(c) Terms of Director Options. Options granted under this Section 6 shall (i) have an
exercise price equal to the closing sale price (for the primary trading session) of the Common
Stock on The Nasdaq Stock Market or the national securities exchange on which the Common Stock is
then traded on the trading date immediately prior to the date of grant (and if the Common Stock is
not then traded on The Nasdaq Stock Market or a national securities exchange, the fair market value
of the Common Stock on such date as determined by the Committee), (ii) vest in at the rate of 50%
on each of the first and second anniversaries of the date of grant, provided that the individual
is serving on the Committee on such date (or in the case of an option granted under Section 6(b),
if earlier, on the date which is one business day prior to date of the Company’s next annual
meeting), provided that no additional vesting shall take place after the Participant ceases to
serve as a director and further provided that the Committee may provide for accelerated vesting in
the case of death or disability, (iii) expire on the earlier of 5 years from the date of grant or
60 days following cessation of service on the Committee and (iv) contain such other terms and
conditions as the Committee shall determine.

(d) Committee Discretion. The Committee retains the specific authority to from time
to time increase or decrease the number of shares subject to options granted under this Section 6
or to grant other award forms as permitted under the Plan, subject to the provisions, subject to
the provisions of Section 4(b)(3).

7. Stock Appreciation Rights.

(a) General. A Stock Appreciation Right, or SAR, is an Award entitling the holder,
upon exercise, to receive an amount in Common Stock or cash or a combination thereof (such form to
be determined by the Committee) determined by reference to appreciation, from and after the date of
grant, in the fair market value of a share of Common Stock. No SAR will become exercisable in
whole or in part in less than one year. The date as of which such appreciation or other measure is
determined shall be the exercise date.

(b) Grants. Stock Appreciation Rights may be granted in tandem with, or independently
of, Options granted under the Plan.

(1) Tandem Awards. When Stock Appreciation Rights are expressly granted in tandem
with Options, (i) the Stock Appreciation Right will be exercisable only at such time or times, and
to the extent, that the related Option is exercisable (except to the extent designated by the
Committee in connection with a Reorganization Event) and will be exercisable in accordance with the
procedure required for exercise of the related Option; (ii) the Stock Appreciation Right will
terminate and no longer be exercisable upon the termination or exercise of the related Option,
except to the extent designated by the Committee in connection with a Reorganization Event and
except that a Stock Appreciation Right granted with respect to less than the full number of shares
covered by an Option will not be reduced until the number of shares as to which the related Option
has been exercised or has terminated exceeds the number of shares not covered by the Stock
Appreciation Right; (iii) the Option will terminate and no longer be exercisable upon the exercise
of the related Stock Appreciation Right; and (iv) the Stock Appreciation Right will be transferable
only with the related Option.

(2) Independent SARs. A Stock Appreciation Right not expressly granted in tandem with
an Option will become exercisable at such time or times, and on such conditions, as the Committee
may specify in the SAR Award.

(c) Exercise. Stock Appreciation Rights may be exercised by delivery to the Company
of a written notice of exercise signed by the proper person or by any other form of notice
(including electronic notice) approved by the Committee, together with any other documents required
by the Committee.

8. Restricted Stock; Restricted Stock Units.

(a) General. The Committee may grant Awards entitling recipients to acquire shares of
Common Stock (“Restricted Stock”), subject to the right of the Company to repurchase all or part of
such shares at their issue price or other stated or formula price (or to require forfeiture of such
shares if issued at no cost) from the recipient in the event that conditions specified by the
Committee in the applicable Award are not satisfied prior to the end of the applicable restriction
period or periods established by the Committee for such Award. Instead of granting Awards for
Restricted Stock, the Committee may grant Awards entitling the recipient to receive shares of
Common Stock to be delivered at the time such shares of Common Stock vest (“Restricted Stock
Units”) (Restricted Stock and Restricted Stock Units are each referred to herein as a “Restricted
Stock Award”).

(b) Terms and Conditions. The Committee shall determine the terms and conditions of a
Restricted Stock Award, including the conditions for repurchase (or forfeiture) and the issue
price, if any.

(c) Limitations on Vesting.

(1) Restricted Stock Awards that vest based on the passage of time alone shall be zero
percent vested prior to the first anniversary of the date of grant, no more than 33-1/3%
vested prior to the second anniversary of the date of grant, and no more than 66-2/3% vested
prior to the third anniversary of the date of grant. Restricted Stock Awards that vest upon
the passage of time and provide for accelerated vesting based on performance shall not vest
prior to the first anniversary of the date of grant. This subsection (c)(1) shall not apply
to (A) Awards granted pursuant to Section 11(i), (B) Awards granted through the assumption
of, or in substitution for, outstanding awards previously granted to individuals who became
employees of the Company as a result of a merger, consolidation, acquisition or other
corporate transaction involving the Company, (C) Awards granted as an inducement to
employment with the Company or in connection with an individual’s promotion to a more senior
position within the Company (as determined in the discretion of the Committee), provided,
however that no more than 7.5% of the total number of shares authorized under the Plan may
be so issued in the aggregate during the term of the Plan, or (D) Awards granted in lieu of
a previously earned cash award.

	 	(2)	 	Notwithstanding any other provision of this Plan, the Committee may, in its
discretion, either at the time a Restricted Stock Award is made or at any time
thereafter, waive its right to repurchase shares of Common Stock (or waive the
forfeiture thereof) or remove or modify any part or all of the restrictions applicable
to the Restricted Stock Award, provided that the Committee may only exercise such
rights in extraordinary circumstances which shall include, without limitation, death or
disability of the Participant; estate planning needs of the Participant; a merger,
consolidation, sale, reorganization, recapitalization, or change in control of the
Company; or any other nonrecurring significant event affecting the Company, a
Participant or the Plan.

	 	(d)	 	Stock Certificates. Any stock certificates issued in respect of
a Restricted Stock Award shall be registered in the name of the Participant
and, unless otherwise determined by the Committee, deposited by the
Participant, together with a stock power endorsed in blank, with the Company
(or its designee). At the expiration of the applicable restriction periods,
the Company (or such designee) shall deliver the certificates no longer subject
to such restrictions to the Participant or if the Participant has died, to the
beneficiary designated, in a manner determined by the Committee, by a
Participant to receive amounts due or exercise rights of the Participant in the
event of the Participant’s death (the “Designated Beneficiary”). In the
absence of an effective designation by a Participant, “Designated Beneficiary”
shall mean the Participant’s estate.

9. Other Stock-Based Awards.

Other Awards of shares of Common Stock, and other Awards that are valued in whole or in part
by reference to, or are otherwise based on, shares of Common Stock or other property, may be
granted hereunder to Participants (“Other Stock Unit Awards”), including without limitation Awards
entitling recipients to receive shares of Common Stock to be delivered in the future. Such Other
Stock Unit Awards shall also be available as a form of payment in the settlement of other Awards
granted under the Plan or as payment in lieu of compensation to which a Participant is otherwise
entitled. Other Stock Unit Awards may be paid in shares of Common Stock or cash, as the Committee
shall determine. Subject to the provisions of the Plan, the Committee shall determine the
conditions of each Other Stock Unit Award, including any purchase price applicable thereto.

10. Adjustments for Changes in Common Stock and Certain Other Events.

(a) Changes in Capitalization. In the event of any stock split, reverse stock split,
stock dividend, recapitalization, combination of shares, reclassification of shares, spin-off or
other similar change in capitalization or event, or any distribution to holders of Common Stock
other than an ordinary cash dividend, (i) the number and class of securities available under this
Plan, (ii) the sub-limits set forth in Section 4(b), (iii) the number and class of securities and
exercise price per share of each outstanding Option and each Option issuable under Section 6, (iv)
the share- and per-share provisions of each Stock Appreciation Right, (v) the repurchase price per
share subject to each outstanding Restricted Stock Award and (vi) the share- and per-share-related
provisions of each outstanding Other Stock Unit Award, shall be appropriately adjusted by the
Company (or substituted Awards may be made, if applicable) to the extent determined by the
Committee.

(b) Reorganization Events.

(1) Definition. A “Reorganization Event” shall mean: (a) any merger or consolidation
of the Company with or into another entity as a result of which all of the Common Stock of the
Company is converted into or exchanged for the right to receive cash, securities or other property
or is cancelled, (b) any exchange of all of the Common Stock of the Company for cash, securities or
other property pursuant to a share exchange transaction or (c) any liquidation or dissolution of
the Company.

(2) Consequences of a Reorganization Event on Awards Other than Restricted Stock
Awards. In connection with a Reorganization Event, the Committee shall take any one or more of
the following actions as to all or any outstanding Awards on such terms as the Committee
determines: (i) provide that Awards shall be assumed, or substantially equivalent Awards shall be
substituted, by the acquiring or succeeding corporation (or an affiliate thereof), (ii) upon
written notice to a Participant, provide that the Participant’s unexercised Options or other
unexercised Awards shall become exercisable in full and will terminate immediately prior to the
consummation of such Reorganization Event unless exercised by the Participant within a specified
period following the date of such notice, (iii) provide that outstanding Awards shall become
realizable or deliverable, or restrictions applicable to an Award shall lapse, in whole or in part
prior to or upon such Reorganization Event, (iv) in the event of a Reorganization Event under the
terms of which holders of Common Stock will receive upon consummation thereof a cash payment for
each share surrendered in the Reorganization Event (the “Acquisition Price”), make or provide for a
cash payment to a Participant equal to (A) the Acquisition Price times the number of shares of
Common Stock subject to the Participant’s Options or other Awards (to the extent the exercise price
does not exceed the Acquisition Price) minus (B) the aggregate exercise price of all such
outstanding Options or other Awards, in exchange for the termination of such Options or other
Awards, (v) provide that, in connection with a liquidation or dissolution of the Company, Awards
shall convert into the right to receive liquidation proceeds (if applicable, net of the exercise
price thereof) and (vi) any combination of the foregoing.

For purposes of clause (i) above, an Option shall be considered assumed if, following
consummation of the Reorganization Event, the Option confers the right to purchase, for each share
of Common Stock subject to the Option immediately prior to the consummation of the Reorganization
Event, the consideration (whether cash, securities or other property) received as a result of the
Reorganization Event by holders of Common Stock for each share of Common Stock held immediately
prior to the consummation of the Reorganization Event (and if holders were offered a choice of
consideration, the type of consideration chosen by the holders of a majority of the outstanding
shares of Common Stock); provided, however, that if the consideration received as a result of the
Reorganization Event is not solely common stock of the acquiring or succeeding corporation (or an
affiliate thereof), the Company may, with the consent of the acquiring or succeeding corporation,
provide for the consideration to be received upon the exercise of Options to consist solely of
common stock of the acquiring or succeeding corporation (or an affiliate thereof) equivalent in
value (as determined by the Committee) to the per share consideration received by holders of
outstanding shares of Common Stock as a result of the Reorganization Event.

To the extent all or any portion of an Option becomes exercisable solely as a result of clause
(ii) above, the Committee may provide that upon exercise of such Option the Participant shall
receive shares subject to a right of repurchase by the Company or its successor at the Option
exercise price; such repurchase right (x) shall lapse at the same rate as the Option would have
become exercisable under its terms and (y) shall not apply to any shares subject to the Option that
were exercisable under its terms without regard to clause (ii) above.

(3) Consequences of a Reorganization Event on Restricted Stock Awards. Upon the
occurrence of a Reorganization Event other than a liquidation or dissolution of the Company, the
repurchase and other rights of the Company under each outstanding Restricted Stock Award shall
inure to the benefit of the Company’s successor and shall apply to the cash, securities or other
property which the Common Stock was converted into or exchanged for pursuant to such Reorganization
Event in the same manner and to the same extent as they applied to the Common Stock subject to such
Restricted Stock Award. Upon the occurrence of a Reorganization Event involving the liquidation or
dissolution of the Company, except to the extent specifically provided to the contrary in the
instrument evidencing any Restricted Stock Award or any other agreement between a Participant and
the Company, all restrictions and conditions on all Restricted Stock Awards then outstanding shall
automatically be deemed terminated or satisfied.

11. General Provisions Applicable to Awards

(a) Transferability of Awards. Awards shall not be sold, assigned, transferred,
pledged or otherwise encumbered by the person to whom they are granted, either voluntarily or by
operation of law, except by will or the laws of descent and distribution or, other than in the case
of an Incentive Stock Option, pursuant to a qualified domestic relations order, and, during the
life of the Participant, shall be exercisable only by the Participant; provided, however, that the
Committee may permit or provide in an Award for the gratuitous transfer of the Award by the
Participant to or for the benefit of any immediate family member, family trust or family
partnership established solely for the benefit of the Participant and/or an immediate family member
thereof if, with respect to such proposed transferee, the Company would be eligible to use a Form
S-8 for the registration of the sale of the Common Stock subject to such Award under the Securities
Act of 1933, as amended; provided, further, that the Company shall not be required to recognize any
such transfer until such time as the Participant and such permitted transferee shall, as a
condition to such transfer, deliver to the Company a written instrument in form and substance
satisfactory to the Company confirming that such transferee shall be bound by all of the terms and
conditions of the Award. References to a Participant, to the extent relevant in the context, shall
include references to authorized transferees.

(b) Documentation. Each Award shall be evidenced in such form (written, electronic or
otherwise) as the Committee shall determine. Each Award may contain terms and conditions in
addition to those set forth in the Plan.

(c) Committee Discretion. Except as otherwise provided by the Plan, each Award may be
made alone or in addition or in relation to any other Award. The terms of each Award need not be
identical, and the Committee need not treat Participants uniformly.

(d) Termination of Status. The Committee shall determine the effect on an Award of
the disability, death, retirement, authorized leave of absence or other change in the employment
or other status of a Participant and the extent to which, and the period during which, the
Participant, or the Participant’s legal representative, conservator, guardian or Designated
Beneficiary, may exercise rights under the Award.

(e) Withholding. Each Participant shall pay to the Company, or make provision
satisfactory to the Company for payment of, any taxes required by law to be withheld in connection
with an Award to such Participant. Except as the Committee may otherwise provide in an Award, for
so long as the Common Stock is registered under the Exchange Act, Participants may satisfy such tax
obligations in whole or in part by delivery of shares of Common Stock, including shares retained
from the Award creating the tax obligation, valued at their Fair Market Value; provided, however,
except as otherwise provided by the Committee, that the total tax withholding where stock is being
used to satisfy such tax obligations cannot exceed the Company’s minimum statutory withholding
obligations (based on minimum statutory withholding rates for federal and state tax purposes,
including payroll taxes, that are applicable to such supplemental taxable income). Shares
surrendered to satisfy tax withholding requirements cannot be subject to any repurchase,
forfeiture, unfulfilled vesting or other similar requirements. The Company may, to the extent
permitted by law, deduct any such tax obligations from any payment of any kind otherwise due to a
Participant.

(f) Amendment of Award. The Committee may amend, modify or terminate any outstanding
Award, including but not limited to, substituting therefor another Award of the same or a different
type, changing the date of exercise or realization, and converting an Incentive Stock Option to a
Nonstatutory Stock Option, provided that the Participant’s consent to such action shall be required
unless the Committee determines that the action, taking into account any related action, would not
materially and adversely affect the Participant.

(g) Conditions on Delivery of Stock. The Company will not be obligated to deliver any
shares of Common Stock pursuant to the Plan or to remove restrictions from shares previously
delivered under the Plan until (i) all conditions of the Award have been met or removed to the
satisfaction of the Company, (ii) in the opinion of the Company’s counsel, all other legal matters
in connection with the issuance and delivery of such shares have been satisfied, including any
applicable securities laws and any applicable stock exchange or stock market rules and regulations,
and (iii) the Participant has executed and delivered to the Company such representations or
agreements as the Company may consider appropriate to satisfy the requirements of any applicable
laws, rules or regulations.

(h) Acceleration. Except as otherwise provided in Section 5, The Committee may at any
time provide that any Award shall become immediately exercisable in full or in part, free of some
or all restrictions or conditions, or otherwise realizable in full or in part, as the case may be.

(i) Performance Conditions.

(1) This Section 11(i) shall be administered by a Committee approved by the Committee, all of
the members of which are “outside directors” as defined by Section 162(m) (the “Section 162(m)
Committee”).

(2) Notwithstanding any other provision of the Plan, if the Section 162(m) Committee
determines, at the time a Restricted Stock Award or Other Stock Unit Award is granted to a
Participant, that such Participant is, or may be as of the end of the tax year in which the Company
would claim a tax deduction in connection with such Award, a Covered Employee (as defined in
Section 162(m)), then the Section 162(m) Committee may provide that this Section 11(i) is
applicable to such Award.

(3) If a Restricted Stock Award or Other Stock Unit Award is subject to this Section 11(i),
then the lapsing of restrictions thereon and the distribution of cash or Shares pursuant thereto,
as applicable, shall be subject to the achievement of one or more objective performance goals
established by the Section 162(m) Committee, which shall be based on the relative or absolute
attainment of specified levels of one or any combination of the following: (a) earnings per share,
(b) return on average equity with respect to a pre-determined peer group, (c) earnings, (d)
earnings growth, (e) revenues, (f) expenses, (g) stock price, (h) achievement of post-acquisition
cost reductions and operating synergies, (i) regulatory compliance, (j) improvement of financial
ratings, (k) achievement of balance sheet objectives, (l) total shareholder return, and may be
absolute in their terms or measured against or in relationship to other companies comparably,
similarly or otherwise situated. Such performance goals may be adjusted to exclude any one or more
of (i) extraordinary items, (ii) gains or losses on the dispositions of discontinued operations,
(iii) the cumulative effects of changes in accounting principles, (iv) the writedown of any asset,
(v) charges for restructuring and rationalization programs and (vi) fluctuations in foreign
currency exchange rates. Such performance goals: (i) may vary by Participant and may be different
for different Awards; (ii) may be particular to a Participant or the department, branch, line of
business, subsidiary or other unit in which the Participant works and may cover such period as may
be specified by the Section 162(m) Committee; and (iii) shall be set by the Section 162(m)
Committee within the time period prescribed by, and shall otherwise comply with the requirements
of, Section 162(m).

(4) Notwithstanding any provision of the Plan, with respect to any Restricted Stock Award or
Other Stock Unit Award that is subject to this Section 11(i), the Section 162(m) Committee may
adjust downwards, but not upwards, the cash or number of Shares payable pursuant to such Award, and
the Section 162(m) Committee may not waive the achievement of the applicable performance goals
except in the case of the death or disability of the Participant.

(5) The Section 162(m) Committee shall have the power to impose such other restrictions on
Awards subject to this Section 11(i) as it may deem necessary or appropriate to ensure that such
Awards satisfy all requirements for “performance-based compensation” within the meaning of Section
162(m)(4)(C) of the Code, or any successor provision thereto.

12. Miscellaneous

(a) No Right To Employment or Other Status. No person shall have any claim or right
to be granted an Award, and the grant of an Award shall not be construed as giving a Participant
the right to continued employment or any other relationship with the Company. The Company
expressly reserves the right at any time to dismiss or otherwise terminate its relationship with a
Participant free from any liability or claim under the Plan, except as expressly provided in the
applicable Award.

(b) No Rights As Stockholder. Subject to the provisions of the applicable Award, no
Participant or Designated Beneficiary shall have any rights as a stockholder with respect to any
shares of Common Stock to be distributed with respect to an Award until becoming the record holder
of such shares. Notwithstanding the foregoing, in the event the Company effects a split of the
Common Stock by means of a stock dividend and the exercise price of and the number of shares
subject to such Option are adjusted as of the date of the distribution of the dividend (rather than
as of the record date for such dividend), then an optionee who exercises an Option between the
record date and the distribution date for such stock dividend shall be entitled to receive, on the
distribution date, the stock dividend with respect to the shares of Common Stock acquired upon such
Option exercise, notwithstanding the fact that such shares were not outstanding as of the close of
business on the record date for such stock dividend.

(c) Effective Date and Term of Plan. The Plan shall become effective on the date on
which it is adopted by the Committee, but no Award may be granted unless and until the Plan has
been approved by the Company’s stockholders. No Awards shall be granted under the Plan after the
completion of 10 years from the earlier of (i) the date on which the Plan was adopted by the
Committee or (ii) the date the Plan was approved by the Company’s stockholders, but Awards
previously granted may extend beyond that date.

(d) Amendment of Plan. The Committee may amend, suspend or terminate the Plan or any
portion thereof at any time; provided that (i) to the extent required by Section 162(m), no Award
granted to a Participant that is intended to comply with Section 162(m) after the date of such
amendment shall become exercisable, realizable or vested, as applicable to such Award, unless and
until such amendment shall have been approved by the Company’s stockholders if required by Section
162(m) (including the vote required under Section 162(m)); (ii) no amendment that would require
stockholder approval under the rules of the NASDAQ may be made effective unless and until such
amendment shall have been approved by the Company’s stockholders; and (iii) if the NASDAQ amends
its corporate governance rules so that such rules no longer require stockholder approval of
“material revisions” to equity compensation plans, then, from and after the effective date of such
amendment to the NASDAQ rules, no amendment to the Plan (A) materially increasing the number of
shares authorized under the Plan (other than pursuant to Section 10), (B) expanding the types of
Awards that may be granted under the Plan, or (C) materially expanding the class of participants
eligible to participate in the Plan shall be effective unless stockholder approval is obtained. In
addition, if at any time the approval of the Company’s stockholders is required as to any other
modification or amendment under Section 422 of the Code or any successor provision with respect to
Incentive Stock Options, the Committee may not effect such modification or amendment without such
approval.

(e) Provisions for Foreign Participants. The Committee may modify Awards or Options
granted to Participants who are foreign nationals or employed outside the United States or
establish subplans or procedures under the Plan to recognize differences in laws, rules,
regulations or customs of such foreign jurisdictions with respect to tax, securities, currency,
employee benefit or other matters.

(f) Compliance With Code Section 409A. No Award shall provide for deferral of
compensation that does not comply with Section 409A of the Code, unless the Committee, at the time
of grant, specifically provides that the Award is not intended to comply with Section 409A of the
Code.

(g) Governing Law. The provisions of the Plan and all Awards made hereunder shall be
governed by and interpreted in accordance with the laws of the State of Delaware, excluding
choice-of-law principles of the law of such state that would require the application of the laws of
a jurisdiction other than such state.EX-10.1

EXHIBIT 10.1

SEVERANCE AND CHANGE IN CONTROL AGREEMENT

This Agreement (the “Agreement”) is entered into as of the 30th day of April, 2009 by and
between Altus Pharmaceuticals Inc., a Delaware corporation (the “Company”), and Thomas J. Phair,
Jr. (the “Executive”).

WHEREAS Executive is employed by the Company, and because of such employment, possesses
detailed knowledge of the Company and its business and operations;

WHEREAS Executive’s continued service to the Company is very important to the future success
of the Company;

WHEREAS the Company desires to enter into this Agreement to provide Executive with certain
financial protection in the event that Executive’s employment terminates under certain
circumstances, and thereby to provide Executive with incentives to remain with the Company

WHEREAS the Board of Directors of the Company (the “Board”) acting through the Compensation
Committee has determined that it is in the best interests of the Company to enter into this
Agreement.

NOW THEREFORE for good and valuable consideration, the receipt and sufficiency of which are
hereby acknowledged, the Company and Executive agree as follows:

1. Definitions.

(a) Cause. As used herein, “Cause” shall include (and is not limited to): (i)
dishonesty with respect to the Company or any affiliate, parent or subsidiary of the Company; (ii)
insubordination; (iii) substantial malfeasance or nonfeasance of duty; (iv) unauthorized disclosure
of confidential information; (v) Executive’s breach of any material provision of any employment,
consulting, advisory, non-disclosure, non-competition, or similar material agreement between
Executive and the Company, which breach, where reasonably subject to cure, is not cured to the
satisfaction of the Board within ten (10) days after notice to Executive by the Company of such
breach; or (vi) conduct substantially prejudicial to the business of the Company or any affiliate,
parent or subsidiary of the Company. The Board shall have sole discretion to determine the
existence of “Cause,” and its determination will be conclusive on Executive and the Company;
provided that the Board may delegate its power to act under this paragraph (a) to a committee of
the Board in which case the determination of such committee shall be conclusive. “Cause” is not
limited to events which have occurred prior to the termination of Executive’s service, nor is it
necessary that the Board’s finding of “Cause” occur prior to such termination. If the Board
determines, subsequent to Executive’s termination of service, that either prior or subsequent to
Executive’s termination Executive engaged in conduct which would constitute “Cause,” then Executive
shall have no right to any benefit or compensation under this Agreement.

(b) Change In Control. As used herein, a “Change in Control” shall mean:

(i) the shareholders of the Company approve: (a) any consolidation or merger of the Company
(x) where the shareholders of the Company, immediately prior to the consolidation or merger, would
not, immediately after the consolidation or merger, beneficially own, directly or indirectly,
shares representing in the aggregate more than 50% of the combined

voting power of all the outstanding securities of the corporation issuing cash or securities in the
consolidation or merger (or of its ultimate parent corporation, if any) or (y) where the members of
the Board, immediately prior to the consolidation or merger, would not, immediately after the
consolidation or merger, constitute more than 50% of the board of directors of the corporation
issuing cash or securities in the consolidation or merger (or of its ultimate parent corporation,
if any); (b) any sale, lease, exchange or other transfer (in one transaction or a series of
transactions contemplated or arranged by any party as a single plan) of all or substantially all of
the assets of the Company; or (c) any plan or proposal for the liquidation or dissolution of the
Company;

(ii) individuals who, as of the date hereof, constitute the entire Board (the “Incumbent
Directors”) cease for any reason to constitute at least 50% of the Board, provided that any
individual becoming a director subsequent to the date hereof whose election, or nomination for
election by the Company’s shareholders, was approved by a vote of at least a majority of the then
Incumbent Directors shall be, for purposes of this Agreement, considered as though such individual
were an Incumbent Director; or

(iii) any “person,” as such term is used in Section 13(d) of the Securities Exchange Act of
1934, as amended (the “Exchange Act”) (other than the Company, any employee benefit plan of the
Company or any entity organized, appointed or established by the Company for or pursuant to the
terms of such plan), together with all “affiliates” and “associates” (as such terms are defined in
Rule 12b-2 under the Exchange Act) of such person, shall become the “beneficial owner” or
“beneficial owners” (as defined in Rules 13d-3 and 13d-5 under the Exchange Act), directly or
indirectly, of securities of the Company representing in the aggregate 25% or more of either: (a)
the then outstanding shares of the Common Stock of the Company or (b) the combined voting power of
all then outstanding securities of the Company having the right under ordinary circumstances to
vote in an election of the Board (“Voting Securities”) (in either such case, other than as a result
of acquisitions of such securities directly from the Company).

Notwithstanding the foregoing, a “Change in Control” of the Company shall not be deemed to
have occurred for purposes of the foregoing clause (iii) solely as the result of an acquisition of
securities by the Company which, by reducing the number of shares of Common Stock or other Voting
Securities outstanding, increases: (a) the proportionate number of shares of Common Stock
beneficially owned by any person to 25% or more of the Common Stock then outstanding, or (b) the
proportionate voting power represented by the Voting Securities beneficially owned by any person to
25% or more of the combined voting power of all then outstanding Voting Securities; provided,
however, that if any person referred to in clause (a) or (b) of this sentence shall thereafter
become the beneficial owner of any additional shares of Common Stock or other Voting Securities
(other than pursuant to a stock split, stock dividend or similar transaction), then a “Change in
Control” shall be deemed to have occurred for purposes of the foregoing clause (iii).

(c) Good Reason. As used herein, a “Good Reason” shall mean: (i) Executive, as a
condition of remaining an employee of the Company, is required to relocate at least 50 miles from
Executive’s then-current location of employment; (ii) there occurs a material adverse change in
Executive’s duties, authority or responsibilities which causes Executive’s position with the
Company to become of significantly less responsibility or authority than Executive’s position was
immediately prior to the Change in Control; or (iii) there occurs a material reduction in
Executive’s base salary from Executive’s base salary received immediately prior to the Change in
Control, provided that any notice of termination by Executive for Good Reason shall be given by
Executive within fifteen (15) days of Executive’s becoming aware of the occurrence of the facts
giving rise to such Good Reason. For purposes of this Agreement, “Good Reason” shall be interpreted
in a manner, and limited to the extent necessary, so that it will not cause adverse tax
consequences for either party with respect to Section 409A of the Internal Revenue Code of 1986, as
amended (“Code Section 409A”), and any successor statute, regulation and guidance thereto.

(d) Base Salary. As used herein, “Base Salary” shall mean Executive’s annual base
salary, excluding reimbursements, bonuses, benefits, and amounts attributable to stock options and
other non-cash compensation.

2. Standard Severance. In the event that Executive’s employment is involuntarily
terminated by action of the Company other than for Cause, Executive shall receive the following
(subject to Executive’s execution of a release of claims as described in Section
7):

(a) Severance Payments. Continuation of payments in an amount equal to Executive’s
then-current Base Salary for a twelve (12) month period (the “Severance Period,” if Section
2 applies) less all customary and required taxes and employment-related deductions, in
accordance with the Company’s normal payroll practices (provided such payments will be made at
least monthly).

(b) Separation Bonus. In the Company’s sole discretion, and conditioned upon
appropriate approval from the Compensation Committee, within forty-five (45) days following
Executive’s termination the Company may pay Executive a separation bonus not to exceed fifty
percent (50%) of the target annual bonus to which Executive may have been entitled for the year in
which Executive is terminated, prorated for the portion of the year in which Executive was
employed, provided any such payments will be made within forty-five (45) days following Executive’s
termination with the Company.

(c) COBRA Payments. Upon completion of the appropriate COBRA forms, and subject to
all the requirements of COBRA, the Company shall continue Executive’s participation in the
Company’s health and dental insurance plans at the Company’s cost (except for Executive’s co-pay,
if any, which shall be deducted from Executive’s severance compensation) for the 18 month COBRA
eligibility period following termination, to the same extent that such insurance is provided to
similarly situated Company executives (but in all events on terms not less advantageous than those
applicable to the Executive as of the second business day preceding the date on which employment
terminates), provided that this benefit will cease and the Company will be under no obligation to
provide it if Executive has become eligible for coverage under another employer’s group coverage,
and Executive hereby agrees to notify the Company promptly and in writing should that occur.

(d) No Duplication. In the event that Executive is eligible for Change in Control
Severance under Section 3 below, Executive shall not be eligible for and shall not
receive the Standard Severance as provided in this Section 2.

3. Change In Control Severance. In the event that a Change in Control occurs and within a
period of one (1) year following the Change in Control, either: (i) Executive’s employment is
involuntarily terminated by action of the Company other than for Cause, or (ii) Executive
terminates Executive’s employment voluntarily for Good Reason, then Executive shall receive the
following (subject to Executive’s execution of a release of claims, as described in Section
7):

(a) Severance Payments. Continuation of payments in an amount equal to Executive’s
then-current Base Salary for a twelve (12) month period (the “Severance Period,” if Section
3 applies) less all customary and required taxes and employment-related deductions, in
accordance with the Company’s normal payroll practices (provided such payments will be made at
least monthly).

(b) Separation Bonus. Within forty-five (45) days following Executive’s termination,
payment of a separation bonus in an amount equal to the target annual bonus to which the Executive
may have been entitled for the year in which Executive is terminated.

(c) COBRA Payments. Upon completion of the appropriate COBRA1/ forms, and
subject to all the requirements of COBRA, continuation of Executive’s participation in the
Company’s health and dental insurance plans at the Company’s cost (except for Executive’s co-pay,
if any, which shall be deducted from Executive’s severance compensation) for the 18 month COBRA
eligibility period following such termination, to the same extent that such insurance is provided
to similarly situated Company executives (but in all events on terms not less advantageous than
those applicable to the Executive as of the second business day preceding the date on which
employment terminates).

(d) Outplacement. Direct payment of up to $15,000 of bona fide outplacement services,
provided that the outplacement company engaged by Executive provides reasonably detailed invoices
for such services to the Sr. Director, Human Resources at the Company within the outplacement
company’s normal billing cycle. Payment is limited to services received by Executive between the
date of Executive’s termination of employment and the date on which Executive begins new full-time
employment, and Executive hereby agrees to notify the Company immediately upon obtaining new
full-time employment, provided that all payments must be made before the end of the second year
following the year in which Executive terminates employment.

(e) No Duplication. In the event that Executive is eligible for Standard Severance
under Section 2 above, Executive shall not be eligible for and shall not receive
the Change in Control Severance as provided in this Section 3.

4. No Severance. In the event that Executive’s employment is terminated for any reason
other than those outlined in Sections 2 or 3, then Executive shall have no
right to the severance payments/benefits provided under this Agreement.

5. Distribution Limitation. If any payment or benefit Executive would receive under this
Agreement, when combined with any other payment or benefit Executive receives pursuant to a Change
in Control (for purposes of this section, a “Payment”) would: (i) constitute a “parachute payment”
within the meaning of Section 280G of the Internal Revenue Code of 1986, as amended (the “Code”);
and (ii) but for this sentence, be subject to the excise tax imposed by Section 4999 of the Code
(the “Excise Tax”), then such Payment shall be either: (x) the full amount of such Payment; or (y)
such lesser amount (with cash payments being reduced before stock option compensation) as would
result in no portion of the Payment being subject to the Excise Tax, whichever of the foregoing
amounts, taking into account the applicable federal, state and local employments taxes, income
taxes, and the Excise Tax, results in Executive’s receipt, on an after-tax basis, of the greater
amount of the Payment notwithstanding that all or some portion of the Payment may be subject to the
Excise Tax.

6. Timing Of Payments. Notwithstanding any other provision with respect to the timing of
payments under Sections 2 or 3, if, at the time of Executive’s
termination, Executive is deemed to be a “specified employee” of the Company (within the meaning of
Code Section 409A(a)(2)(B)(i) and any successor statute, regulation and guidance thereto (“Code
Section 409A”)), then limited only to the extent necessary to comply with the requirements of Code
Section 409A, any payments to which Executive may become entitled under Sections 2
or 3 which are subject to Code Section 409A (and not otherwise exempt from its application)
will be withheld until the first (1st) business day of the seventh (7th) month following the
termination of Executive’s employment, at which time Executive shall be paid an aggregate amount
equal to the accumulated, but unpaid, payments otherwise due to Executive under the terms of
Sections 2 or 3.

7. Release of Claims. The Company shall not be obligated to pay Executive any of the
compensation set forth in Sections 2 and 3 unless and until Executive has
executed a timely full and general release of all claims against the Company and any affiliate,
parent or subsidiary, and its and their officers, directors, employees, and agents, in a form
satisfactory to the Company.

8. Restrictive Covenants. Executive acknowledges and agrees that this Agreement provides
Executive with payments and benefits above and beyond those which the Company already is providing
Executive. In exchange for the payments and benefits provided herein, as well as other good and
valuable consideration, Executive agrees to the following restrictive covenants:

(a) While Executive is employed by the Company and for the term of the Severance Period (the
“Non-Competition Period”), the Executive shall not, directly or indirectly, whether as owner,
partner, investor, consultant, agent, employee, co-venturer or otherwise, compete with the Company
or any affiliate, parent or subsidiary of the Company or undertake any planning for any business
competitive with the Company or any affiliate, parent or subsidiary of the Company. For the
purpose of this section, “compete” or “competitive” means to engage or participate (whether for
compensation or without compensation) in any commercial research or commercial project which is the
same or substantially similar (in purpose, objective or result) to any research or project in which
the Executive engaged or participated in, for or on behalf of the Company or any affiliate, parent
or subsidiary of the Company during the Non-Competition Period.

(b) During the Non-Competition Period, the Executive shall not recruit or otherwise solicit or
induce any employees of the Company or any affiliate, parent or subsidiary of the Company to
terminate their employment with, or otherwise cease their relationships with, the Company or any
affiliate, parent or subsidiary of the Company.

(c) The restrictions against competition set forth in paragraph 8(a) are considered by the
parties to be reasonable for the purposes of protecting the business of the Company.  However, if
any such restriction is found by any court of competent jurisdiction to be unenforceable because it
extends for too long a period of time or over too great a range of activities or in too broad a
geographic area, it shall be interpreted to extend only over the maximum period of time, range of
activities or geographic areas as to which it may be enforceable.

9. No Impact On Employment Status. This Agreement is not intended to confer, and shall
not be interpreted as conferring, any additional employment rights on Executive, and has no impact
on either party’s right to terminate Executive’s employment under contract or applicable law.

10. Enforceability; Reduction. If any provision of this Agreement shall be deemed invalid
or unenforceable as written, this Agreement shall be construed, to the greatest extent possible, or
modified, to the extent allowable by law, in a manner which shall render it valid and enforceable
and any limitation on the scope or duration of any provision necessary to make it valid and
enforceable shall be deemed to be a part thereof. No invalidity or unenforceability of any
provision contained herein shall affect any other portion of this Agreement.

11. Notices.

(a) All notices, requests, consents and other communications hereunder shall be in writing,
shall be addressed to the receiving party’s address set forth below or to such other address as a
party may designate by notice hereunder, and shall be either (i) delivered by hand, (ii) made by
telex, telecopy or facsimile transmission, (iii) sent by overnight courier, or (iv) sent by
registered or certified mail, return receipt requested, postage prepaid.

If to the Company:

Chief Executive Officer

Altus Pharmaceuticals Inc.

610 Lincoln Street

Waltham, MA 02451

With a copy to:

General Counsel

Altus Pharmaceuticals Inc.

610 Lincoln Street125

Waltham, MA 02451

If to Executive:

Thomas J. Phair, Jr.

Altus Pharmaceuticals Inc.

610 Lincoln Street125

Waltham, MA 02451

(b) All notices, requests, consents and other communications hereunder shall be deemed to have
been given either (i) if by hand, at the time of the delivery thereof to the receiving party at the
address of such party set forth above, (ii) if made by telex, telecopy or facsimile transmission,
at the time that receipt thereof has been acknowledged by electronic confirmation or otherwise,
(iii) if sent by overnight courier, on the next business day following the day such notice is
delivered to the courier service, or (iv) if sent by registered or certified mail, on the 5th
business day following the day such mailing is made.

12. Entire Agreement / No Duplication of Compensation or Benefits. This Agreement, along
with any prior employee, non-disclosure and invention agreement entered into between the Executive
and the Company (other than noncompetition or nonsolicitation covenants contained therein which are
superceded by this Agreement), embodies the entire agreement and understanding between the parties
hereto with respect to the subject matter hereof and supersedes all prior oral or written
agreements and understandings relating to the subject matter hereof. No statement, representation,
warranty, covenant or agreement of any kind not expressly set forth in this Agreement shall affect,
or be used to interpret, change or restrict, the express terms and provisions of this Agreement.
The terms of Sections 2 and 3 above shall replace any agreement, policy or practice
which otherwise would obligate the Company to provide any severance compensation and/or benefits to
Executive, provided that this provision shall not be construed to otherwise limit Executive’s
rights to payments or benefits provided under any pension plan (as defined in Section 3(2) of the
Employee Retirement Income Security Act of 1974, as amended), deferred compensation, stock, stock
option or similar plan sponsored by the Company, and further provided, that notwithstanding
anything in this Agreement to the contrary, the Company’s obligations to the Executive under this
Agreement shall be reduced by an amount equal to the amount, if any, paid or due and payable to the
Executive pursuant to the Company’s Executive Severance Policy dated April 30, 2009, and no
benefits under this Agreement shall be paid to the extent they would duplicate amounts payable
pursuant to such Executive Severance Policy.

13. Modifications and Amendments. The terms and provisions of this Agreement may be
modified or amended only by written agreement executed by all parties hereto. Any such amendment
shall comply with the requirements of Code Section 409A, if applicable.

14. Waivers and Consents. The terms and provisions of this Agreement may be waived, or
consent for the departure therefrom granted, only by written document executed by the party
entitled to the benefits of such terms or provisions. No such waiver or consent shall be deemed to
be or shall constitute a waiver or consent with respect to any other terms or provisions of this
Agreement, whether or not similar. Each such waiver or consent shall be effective only in the
specific instance and for the purpose for which it was given, and shall not constitute a continuing
waiver or consent.

15. Assignment. The rights and obligations under this Agreement may not be assigned by
either party hereto without the prior written consent of the other party.

16. Benefit. All statements, representations, warranties, covenants and agreements in this
Agreement shall be binding on the parties hereto and shall inure to the benefit of the respective
successors and permitted assigns of each party hereto. Nothing in this Agreement shall be
construed to create any rights or obligations except among the parties hereto, and no person or
entity shall be regarded as a third-party beneficiary of this Agreement.

17. Arbitration. Any controversy, dispute or claim arising out of or in connection with
this Agreement will be settled by final and binding arbitration to be conducted in Boston,
Massachusetts pursuant to the national rules for the resolution of employment disputes of the
American Arbitration Association then in effect. The decision or award in any such arbitration
will be final and binding upon the parties, and judgment upon such decision or award may be entered
in any court of competent jurisdiction, or application may be made to any such court for judicial
acceptance of such decision or award and an order of enforcement. In the event that any procedural
matter is not covered by the aforesaid rules, the procedural law of Massachusetts will govern. Any
disagreement as to whether a particular dispute is arbitrable under this Agreement shall itself be
subject to arbitration in accordance with the procedures set forth herein. Notwithstanding the
foregoing, any right or obligation arising out of or concerning any separate contract or agreement
between the parties (including but not limited to any employee, non-disclosure and invention
agreement) shall be decided in accordance with the dispute resolution mechanism provided for by
such contract or agreement.

18. Governing Law / Jurisdiction / Service of Process. This Agreement and the rights and
obligations of the parties hereunder shall be construed in accordance with and governed by the law
of the Commonwealth of Massachusetts, without giving effect to the conflict of law principles
thereof. Any legal action or proceeding with respect to this Agreement that is not subject to
arbitration pursuant to Section 17 will be brought in the courts of the
Commonwealth of Massachusetts in Middlesex Country or of the United States of America for the
District of Massachusetts, sitting in Boston. By execution and delivery of this Agreement, each of
the parties hereto accepts for itself and in respect of its property, generally and
unconditionally, the exclusive jurisdiction of the aforesaid courts. Each of the parties hereto
irrevocably consents to the service of process of any of the aforementioned courts in any such
action or proceeding by the mailing of copies thereof by certified mail, postage prepaid, to the
party at its address set forth in Section 11.

19. Counterparts. This Agreement may be executed in one or more counterparts, and by
different parties hereto on separate counterparts, each of which shall be deemed an original, but
all of which together shall constitute one and the same instrument.

[REMAINDER OF PAGE INTENTIONALLY LEFT BLANK]

1/ “COBRA” is the Consolidated Omnibus Budget
Reconciliation Act of 1985, as amended.

1

IN WITNESS WHEREOF, the parties have executed this Agreement as of the day and year first
above written.

ALTUS PHARMACEUTICALS INC.

By:      /s/ Georges Gemayel—

Date:       4/30/09      

EXECUTIVE:

      /s/ Thomas J. Phair, Jr.      

Thomas J. Phair, Jr.

Date:       4/30/09      

2

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