QuickLinks -- Click here to rapidly navigate through this document

EXHIBIT 10.1

        HELICOS BIOSCIENCES CORPORATION

--------------------------------------------------------------------------------

2007 STOCK OPTION AND INCENTIVE PLAN

SECTION 1.    GENERAL PURPOSE OF THE PLAN; DEFINITIONS

        The name of the plan is the Helicos BioSciences Corporation 2007 Stock
Option and Incentive Plan (the "Plan"). The purpose of the Plan is to encourage
and enable the officers, employees, Non-Employee Directors and other key persons
(including consultants and prospective employees) of Helicos BioSciences
Corporation (the "Company") and its Subsidiaries upon whose judgment, initiative
and efforts the Company largely depends for the successful conduct of its
business to acquire a proprietary interest in the Company. It is anticipated
that providing such persons with a direct stake in the Company's welfare will
assure a closer identification of their interests with those of the Company and
its stockholders, thereby stimulating their efforts on the Company's behalf and
strengthening their desire to remain with the Company.

        The following terms shall be defined as set forth below:

        "Act" means the Securities Act of 1933, as amended, and the rules and
regulations thereunder.

        "Administrator" means either the Board or the compensation committee of
the Board or a similar committee performing the functions of the compensation
committee and which is comprised of not less than two Non-Employee Directors who
are independent.

        "Award" or "Awards," except where referring to a particular category of
grant under the Plan, shall include Incentive Stock Options, Non-Qualified Stock
Options, Stock Appreciation Rights, Deferred Stock Awards, Restricted Stock
Awards, Unrestricted Stock Awards, Cash-based Awards and Dividend Equivalent
Rights.

        "Award Agreement" means a written or electronic agreement setting forth
the terms and provisions applicable to an Award granted under the Plan. Each
Award Agreement is subject to the terms and conditions of the Plan.

        "Board" means the Board of Directors of the Company.

        "Cash-based Award" means an Award entitling the recipient to receive a
cash-denominated payment.

        "Code" means the Internal Revenue Code of 1986, as amended, and any
successor Code, and related rules, regulations and interpretations.

        "Covered Employee" means an employee who is a "Covered Employee" within
the meaning of Section 162(m) of the Code.

        "Deferred Stock Award" means an Award of phantom stock units to a
grantee.

        "Dividend Equivalent Right" means an Award entitling the grantee to
receive credits based on cash dividends that would have been paid on the shares
of Stock specified in the Dividend Equivalent Right (or other award to which it
relates) if such shares had been issued to and held by the grantee.

        "Effective Date" means the date on which the Plan is approved by
stockholders as set forth in Section 19.

        "Exchange Act" means the Securities Exchange Act of 1934, as amended,
and the rules and regulations thereunder.

        "Fair Market Value" of the Stock on any given date means the fair market
value of the Stock determined in good faith by the Administrator; provided,
however, that if the Stock is admitted to quotation on the National Association
of Securities Dealers Automated Quotation System ("NASDAQ"), NASDAQ Global
Market or another national securities exchange, the determination

--------------------------------------------------------------------------------

shall be made by reference to market quotations. If there are no market
quotations for such date, the determination shall be made by reference to the
last date preceding such date for which there are market quotations; provided
further, however, that if the date for which Fair Market Value is determined is
the first day when trading prices for the Stock are reported on a national
securities exchange, the Fair Market Value shall be the "Price to the Public"
(or equivalent) set forth on the cover page for the final prospectus relating to
the Company's Initial Public Offering.

        "Incentive Stock Option" means any Stock Option designated and qualified
as an "incentive stock option" as defined in Section 422 of the Code.

        "Initial Public Offering" means the consummation of the first fully
underwritten, firm commitment public offering pursuant to an effective
registration statement under the Act covering the offer and sale by the Company
of its equity securities, or such other event as a result of or following which
the Stock shall be publicly held.

        "Non-Employee Director" means a member of the Board who is not also an
employee of the Company or any Subsidiary.

        "Non-Qualified Stock Option" means any Stock Option that is not an
Incentive Stock Option.

        "Option" or "Stock Option" means any option to purchase shares of Stock
granted pursuant to Section 5.

        "Restricted Stock Award" means an Award entitling the recipient to
acquire, at such purchase price (which may be zero) as determined by the
Administrator, shares of Stock subject to such restrictions and conditions as
the Administrator may determine at the time of grant.

        "Sale Event" shall mean (i) the sale of all or substantially all of the
assets of the Company on a consolidated basis to an unrelated person or entity,
(ii) a merger, reorganization or consolidation in which the outstanding shares
of Stock are converted into or exchanged for securities of the successor entity
and the holders of the Company's outstanding voting power immediately prior to
such transaction do not own a majority of the outstanding voting power of the
successor entity immediately upon completion of such transaction, or (iii) the
sale of all of the Stock of the Company to an unrelated person or entity.

        "Sale Price" means the value as determined by the Administrator of the
consideration payable, or otherwise to be received by stockholders, per share of
Stock pursuant to a Sale Event.

        "Section 409A" means Section 409A of the Code and the regulations and
other guidance promulgated thereunder.

        "Stock" means the Common Stock, par value $0.001 per share, of the
Company, subject to adjustments pursuant to Section 3.

        "Stock Appreciation Right" means an Award entitling the recipient to
receive shares of Stock having a value equal to the excess of the Fair Market
Value of the Stock on the date of exercise over the exercise price of the Stock
Appreciation Right multiplied by the number of shares of Stock with respect to
which the Stock Appreciation Right shall have been exercised.

        "Subsidiary" means any corporation or other entity (other than the
Company) in which the Company has at least a 50 percent interest, either
directly or indirectly.

        "Ten Percent Owner" means an employee who owns or is deemed to own (by
reason of the attribution rules of Section 424(d) of the Code) more than
10 percent of the combined voting power of all classes of stock of the Company
or any parent or subsidiary corporation.

        "Unrestricted Stock Award" means an Award of shares of Stock free of any
restrictions.

2

--------------------------------------------------------------------------------

SECTION 2.    ADMINISTRATION OF PLAN; ADMINISTRATOR AUTHORITY TO SELECT GRANTEES
AND DETERMINE AWARDS

        (a)    Administration of Plan.    The Plan shall be administered by the
Administrator.

        (b)    Powers of Administrator.    The Administrator shall have the
power and authority to grant Awards consistent with the terms of the Plan,
including the power and authority:

        (i)    to select the individuals to whom Awards may from time to time be
granted;

        (ii)   to determine the time or times of grant, and the extent, if any,
of Incentive Stock Options, Non-Qualified Stock Options, Stock Appreciation
Rights, Restricted Stock Awards, Deferred Stock Awards, Unrestricted Stock
Awards, Cash-based Awards and Dividend Equivalent Rights, or any combination of
the foregoing, granted to any one or more grantees;

        (iii)  to determine the number of shares of Stock to be covered by any
Award;

        (iv)  to determine and modify from time to time the terms and
conditions, including restrictions, not inconsistent with the terms of the Plan,
of any Award, which terms and conditions may differ among individual Awards and
grantees, and to approve the form of written instruments evidencing the Awards;

        (v)   to accelerate at any time the exercisability or vesting of all or
any portion of any Award;

        (vi)  subject to the provisions of Section 5(a)(ii), to extend at any
time the period in which Stock Options may be exercised; and

        (vii) at any time to adopt, alter and repeal such rules, guidelines and
practices for administration of the Plan and for its own acts and proceedings as
it shall deem advisable; to interpret the terms and provisions of the Plan and
any Award (including related written instruments); to make all determinations it
deems advisable for the administration of the Plan; to decide all disputes
arising in connection with the Plan; and to otherwise supervise the
administration of the Plan.

        All decisions and interpretations of the Administrator shall be binding
on all persons, including the Company and Plan grantees.

        (c)    Delegation of Authority to Grant Options.    Subject to
applicable law, the Administrator, in its discretion, may delegate to the Chief
Executive Officer of the Company all or part of the Administrator's authority
and duties with respect to the granting of Options, to individuals who are
(i) not subject to the reporting and other provisions of Section 16 of the
Exchange Act and (ii) not Covered Employees. Any such delegation by the
Administrator shall include a limitation as to the amount of Options that may be
granted during the period of the delegation and shall contain guidelines as to
the determination of the exercise price and the vesting criteria. The
Administrator may revoke or amend the terms of a delegation at any time but such
action shall not invalidate any prior actions of the Administrator's delegate or
delegates that were consistent with the terms of the Plan.

        (d)    Award Agreement.    Awards under the Plan shall be evidenced by
Award Agreements that set forth the terms, conditions and limitations for each
Award which may include, without limitation, the term of an Award, the
provisions applicable in the event employment or service terminates, and the
Company's authority to unilaterally or bilaterally amend, modify, suspend,
cancel or rescind an Award.

        (e)    Indemnification.    Neither the Board nor the Administrator, nor
any member of either or any delegate thereof, shall be liable for any act,
omission, interpretation, construction or determination made in good faith in
connection with the Plan, and the members of the Board and the Administrator
(and any delegate thereof) shall be entitled in all cases to indemnification and
reimbursement by the Company in respect of any claim, loss, damage or expense
(including, without limitation, reasonable

3

--------------------------------------------------------------------------------

attorneys' fees) arising or resulting therefrom to the fullest extent permitted
by law and/or under the Company's articles or bylaws or any directors' and
officers' liability insurance coverage which may be in effect from time to time
and/or any indemnification agreement between such individual and the Company.

        (f)    Foreign Award Recipients.    Notwithstanding any provision of the
Plan to the contrary, in order to comply with the laws in other countries in
which the Company and its Subsidiaries operate or have employees or other
individuals eligible for Awards, the Administrator, in its sole discretion,
shall have the power and authority to: (i) determine which Subsidiaries shall be
covered by the Plan; (ii) determine which individuals outside the United States
are eligible to participate in the Plan; (iii) modify the terms and conditions
of any Award granted to individuals outside the United States to comply with
applicable foreign laws; (iv) establish subplans and modify exercise procedures
and other terms and procedures, to the extent the Administrator determines such
actions to be necessary or advisable (and such subplans and/or modifications
shall be attached to this Plan as appendices); provided, however, that no such
subplans and/or modifications shall increase the share limitations contained in
Section 3(a) hereof; and (v) take any action, before or after an Award is made,
that the Administrator determines to be necessary or advisable to obtain
approval or comply with any local governmental regulatory exemptions or
approvals. Notwithstanding the foregoing, the Administrator may not take any
actions hereunder, and no Awards shall be granted, that would violate the
Exchange Act or any other applicable United States securities law, the Code, or
any other applicable United States governing statute or law.

SECTION 3.    STOCK ISSUABLE UNDER THE PLAN; MERGERS; SUBSTITUTION

        (a)    Stock Issuable.    The maximum number of shares of Stock reserved
and available for issuance under the Plan shall be the sum of (i) 6,481,198
shares, (ii) the number of Shares under the Company's 2003 Stock Option and
Incentive Plan (the "2003 Plan") which are not needed to fulfill the Company's
obligations for awards issued under the 2003 Plan as a result of forfeiture,
expiration, cancellation, termination or net issuances of awards thereunder, and
(iii) on January 1, 2008 and on each January 1 thereafter, an additional number
of shares equal to the lower of (A) four and one-half percent (4.5%) of the
outstanding number of shares of Stock on the immediately preceding December 31,
or (B) such lower number of shares of Stock as may be determined by the Board of
Directors, in each case subject to adjustment as provided in Section 3(b). For
purposes of this limitation, the shares of Stock underlying any Awards that are
forfeited, canceled, held back upon exercise of an Option or settlement of an
Award to cover the exercise price or tax withholding, reacquired by the Company
prior to vesting, satisfied without the issuance of Stock or otherwise
terminated (other than by exercise) shall be added back to the shares of Stock
available for issuance under the Plan. Subject to such overall limitations,
shares of Stock may be issued up to such maximum number pursuant to any type or
types of Award; provided, however, that (i) Incentive Stock Options may be
granted with respect to no more than 6,431,434 shares, plus on each January 1,
starting January 1, 2008, an additional number of shares equal to the lesser of
(A) four and one-half percent (4.5%) of the outstanding number of shares of
Stock on the immediately preceding December 31 and (B) 3,150,000 shares of Stock
and (ii) Stock Options or Stock Appreciation Rights with respect to no more than
6,500,000 shares of Stock may be granted to any one individual grantee during
any one calendar year period. The shares available for issuance under the Plan
may be authorized but unissued shares of Stock or shares of Stock reacquired by
the Company.

        (b)    Changes in Stock.    Subject to Section 3(c) hereof, if, as a
result of any reorganization, recapitalization, reclassification, stock
dividend, stock split, reverse stock split or other similar change in the
Company's capital stock, the outstanding shares of Stock are increased or
decreased or are exchanged for a different number or kind of shares or other
securities of the Company, or additional shares or new or different shares or
other securities of the Company or other non-cash assets are

4

--------------------------------------------------------------------------------

distributed with respect to such shares of Stock or other securities, or, if, as
a result of any merger or consolidation, sale of all or substantially all of the
assets of the Company, the outstanding shares of Stock are converted into or
exchanged for securities of the Company or any successor entity (or a parent or
subsidiary thereof), the Administrator shall make an appropriate or
proportionate adjustment in (i) the maximum number of shares reserved for
issuance under the Plan, (ii) the number of Stock Options or Stock Appreciation
Rights that can be granted to any one individual grantee, (iii) the number and
kind of shares or other securities subject to any then outstanding Awards under
the Plan, (iv) the repurchase price, if any, per share subject to each
outstanding Restricted Stock Award, and (v) the price for each share subject to
any then outstanding Stock Options and Stock Appreciation Rights under the Plan,
without changing the aggregate exercise price (i.e., the exercise price
multiplied by the number of Stock Options and Stock Appreciation Rights) as to
which such Stock Options and Stock Appreciation Rights remain exercisable. The
Administrator shall also make equitable or proportionate adjustments in the
number of shares subject to outstanding Awards and the exercise price and the
terms of outstanding Awards to take into consideration cash dividends paid other
than in the ordinary course or any other extraordinary corporate event. The
adjustment by the Administrator shall be final, binding and conclusive. No
fractional shares of Stock shall be issued under the Plan resulting from any
such adjustment, but the Administrator in its discretion may make a cash payment
in lieu of fractional shares.

        (c)    Mergers and Other Transactions.    Except as the Administrator
may otherwise specify with respect to particular Awards in the relevant Award
documentation, in the case of and subject to the consummation of a Sale Event,
the Administrator shall as to outstanding Awards (on the same basis or on
different bases as the Administrator shall specify), make appropriate provision
for the assumption or continuation of Awards theretofore granted by the
successor entity, or the substitution of such Awards with new Awards of the
successor entity or parent thereof, with appropriate adjustment as to the number
and kind of shares and, if appropriate, the per share exercise prices, as the
Administrator shall specify. In addition to or in lieu of the foregoing, the
Administrator may provide that, upon the effective time of the Sale Event, the
Plan and all outstanding Awards granted hereunder shall terminate. In the event
of such termination, (i) the Company shall have the option (in its sole
discretion) to make or provide for a cash payment to the grantees holding
Options and Stock Appreciation Rights, in exchange for the cancellation thereof,
in an amount equal to the difference between (A) the Sale Price multiplied by
the number of shares of Stock subject to outstanding Options and Stock
Appreciation Rights (to the extent then exercisable (after taking into account
any acceleration hereunder) at prices not in excess of the Sale Price) and
(B) the aggregate exercise price of all such outstanding Options and Stock
Appreciation Rights; or (ii) each grantee shall be permitted, within a specified
period of time prior to the consummation of the Sale Event as determined by the
Administrator, to exercise all outstanding Options and Stock Appreciation Rights
held by such grantee; provided, however, that, in the case of this clause (ii),
all Options and Stock Appreciation Rights that are not exercisable immediately
prior to the effective time of the Sale Event shall become fully exercisable as
of the effective time of the Sale Event.

        (d)    Substitute Awards.    The Administrator may grant Awards under
the Plan in substitution for stock and stock based awards held by employees,
directors or other key persons of another corporation in connection with the
merger or consolidation of the employing corporation with the Company or a
Subsidiary or the acquisition by the Company or a Subsidiary of property or
stock of the employing corporation. The Administrator may direct that the
substitute awards be granted on such terms and conditions as the Administrator
considers appropriate in the circumstances. Any substitute Awards granted under
the Plan shall not count against the share limitation set forth in Section 3(a).

5

--------------------------------------------------------------------------------

SECTION 4.    ELIGIBILITY

        Grantees under the Plan will be such full or part-time officers and
other employees, Non-Employee Directors and key persons (including consultants
and prospective employees) of the Company and its Subsidiaries as are selected
from time to time by the Administrator in its sole discretion.

SECTION 5.    STOCK OPTIONS

        Any Stock Option granted under the Plan shall be in such form as the
Administrator may from time to time approve.

        Stock Options granted under the Plan may be either Incentive Stock
Options or Non-Qualified Stock Options. Incentive Stock Options may be granted
only to employees of the Company or any Subsidiary that is a "subsidiary
corporation" within the meaning of Section 424(f) of the Code. To the extent
that any Option does not qualify as an Incentive Stock Option, it shall be
deemed a Non-Qualified Stock Option.

        (a)    Stock Options Granted to Employees and Key Persons.    The
Administrator in its discretion may grant Stock Options to eligible employees
and key persons of the Company or any Subsidiary. Stock Options granted pursuant
to this Section 5(a) shall be subject to the following terms and conditions and
shall contain such additional terms and conditions, not inconsistent with the
terms of the Plan, as the Administrator shall deem desirable. If the
Administrator so determines, Stock Options may be granted in lieu of cash
compensation at the optionee's election, subject to such terms and conditions as
the Administrator may establish.

                (i)    Exercise Price.    The exercise price per share for the
Stock covered by a Stock Option granted pursuant to this Section 5(a) shall be
determined by the Administrator at the time of grant but shall not be less than
100 percent of the Fair Market Value on the date of grant. In the case of an
Incentive Stock Option that is granted to a Ten Percent Owner, the option price
of such Incentive Stock Option shall be not less than 110 percent of the Fair
Market Value on the grant date.

                (ii)    Option Term.    The term of each Stock Option shall be
fixed by the Administrator, but no Stock Option shall be exercisable more than
ten years after the date the Stock Option is granted. In the case of an
Incentive Stock Option that is granted to a Ten Percent Owner, the term of such
Stock Option shall be no more than five years from the date of grant.

                (iii)    Exercisability; Rights of a Stockholder.    Stock
Options shall become exercisable at such time or times, whether or not in
installments, as shall be determined by the Administrator at or after the grant
date. The Administrator may at any time accelerate the exercisability of all or
any portion of any Stock Option. An optionee shall have the rights of a
stockholder only as to shares acquired upon the exercise of a Stock Option and
not as to unexercised Stock Options.

                (iv)    Method of Exercise.    Stock Options may be exercised in
whole or in part, by giving written notice of exercise to the Company,
specifying the number of shares to be purchased. Payment of the purchase price
may be made by one or more of the following methods to the extent provided in
the Option Award Agreement:

        (A)  In cash, by certified or bank check or other instrument acceptable
to the Administrator;

        (B)  Through the delivery (or attestation to the ownership) of shares of
Stock that have been purchased by the optionee on the open market or that are
beneficially owned by the optionee and are not then subject to restrictions
under any Company plan. Such surrendered shares shall be valued at Fair Market
Value on the exercise date. To the extent required to avoid variable accounting
treatment under FAS 123R or other applicable accounting rules, such surrendered
shares shall have been owned by the optionee for at least six months; or

6

--------------------------------------------------------------------------------

        (C)  By the optionee delivering to the Company a properly executed
exercise notice together with irrevocable instructions to a broker to promptly
deliver to the Company cash or a check payable and acceptable to the Company for
the purchase price; provided that in the event the optionee chooses to pay the
purchase price as so provided, the optionee and the broker shall comply with
such procedures and enter into such agreements of indemnity and other agreements
as the Administrator shall prescribe as a condition of such payment procedure.

Payment instruments will be received subject to collection. The transfer to the
optionee on the records of the Company or of the transfer agent of the shares of
Stock to be purchased pursuant to the exercise of a Stock Option will be
contingent upon receipt from the optionee (or a purchaser acting in his stead in
accordance with the provisions of the Stock Option) by the Company of the full
purchase price for such shares and the fulfillment of any other requirements
contained in the Option Award Agreement or applicable provisions of laws
(including the satisfaction of any withholding taxes that the Company is
obligated to withhold with respect to the optionee). In the event an optionee
chooses to pay the purchase price by previously-owned shares of Stock through
the attestation method, the number of shares of Stock transferred to the
optionee upon the exercise of the Stock Option shall be net of the number of
shares attested to. In the event that the Company establishes, for itself or
using the services of a third party, an automated system for the exercise of
Stock Options, such as a system using an internet website or interactive voice
response, then the paperless exercise of Stock Options may be permitted through
the use of such an automated system.

        (v)    Annual Limit on Incentive Stock Options.    To the extent
required for "incentive stock option" treatment under Section 422 of the Code,
the aggregate Fair Market Value (determined as of the time of grant) of the
shares of Stock with respect to which Incentive Stock Options granted under this
Plan and any other plan of the Company or its parent and subsidiary corporations
become exercisable for the first time by an optionee during any calendar year
shall not exceed $100,000. To the extent that any Stock Option exceeds this
limit, it shall constitute a Non-Qualified Stock Option.

        (b)    Stock Options Granted to Non-Employee Directors.    The
Administrator in its discretion may grant Non-Qualified Stock Options to
Non-Employee Directors. Non-Qualified Stock Options granted pursuant to this
Section 5(b) shall be subject to the following terms and conditions and shall
contain such additional terms and conditions, not inconsistent with the terms of
the Plan, as the Administrator shall deem desirable. If the Administrator so
determines, Non-Qualified Stock Options may be granted in lieu of cash
compensation at the optionee's election, subject to such terms and conditions as
the Administrator may establish.

                (i)    Exercise Price.    The exercise price per share for the
Stock covered by a Stock Option granted pursuant to this Section 5(b) shall be
no less than 100 percent of the Fair Market Value of the Stock on the date the
Stock Option is granted.

                (ii)    Exercise; Termination.    

        (A)  Options shall become exercisable at such time or times, whether or
not in installments, as shall be determined by the Administrator at or after the
grant date. The Administrator may at any time accelerate the exercisability of
all or any portion of any Stock Option. A Stock Option issued under this
Section 5(b) shall not be exercisable after the expiration of ten years from the
date of grant.

        (B)  Stock Options granted under this Section 5(b) may be exercised only
by written notice to the Company specifying the number of shares to be
purchased. Payment of the full purchase price of the shares to be purchased may
be made by one or more of the methods specified in Section 5(a)(iv). An optionee
shall have the rights of a stockholder only as to shares acquired upon the
exercise of a Stock Option and not as to unexercised Stock Options.

7

--------------------------------------------------------------------------------

SECTION 6.    STOCK APPRECIATION RIGHTS

        (a)    Exercise Price of Stock Appreciation Rights.    The exercise
price of a Stock Appreciation Right shall not be less than 100 percent of the
Fair Market Value of the Stock on the date of grant (or more than the Stock
Option exercise price per share, if the Stock Appreciation Right was granted in
tandem with a Stock Option).

        (b)    Grant and Exercise of Stock Appreciation Rights.    Stock
Appreciation Rights may be granted by the Administrator in tandem with, or
independently of, any Stock Option granted pursuant to Section 5 of the Plan. In
the case of a Stock Appreciation Right granted in tandem with a Non-Qualified
Stock Option, such Stock Appreciation Right may be granted either at or after
the time of the grant of such Option. In the case of a Stock Appreciation Right
granted in tandem with an Incentive Stock Option, such Stock Appreciation Right
may be granted only at the time of the grant of the Option.

        A Stock Appreciation Right or applicable portion thereof granted in
tandem with a Stock Option shall terminate and no longer be exercisable upon the
termination or exercise of the related Option.

        (c)    Terms and Conditions of Stock Appreciation Rights.    Stock
Appreciation Rights shall be subject to such terms and conditions as shall be
determined from time to time by the Administrator, subject to the following:

        (i)    Stock Appreciation Rights granted in tandem with Options shall be
exercisable at such time or times and to the extent that the related Stock
Options shall be exercisable.

        (ii)   Upon exercise of a Stock Appreciation Right, the applicable
portion of any related Option shall be surrendered.

        (iii)  Stock Appreciation Rights may have a term of no more than ten
years.

SECTION 7.    RESTRICTED STOCK AWARDS

        (a)    Nature of Restricted Stock Awards.    The Administrator shall
determine the restrictions and conditions applicable to each Restricted Stock
Award at the time of grant. Conditions may be based on continuing employment (or
other service relationship) and/or achievement of pre-established performance
goals and objectives. The grant of a Restricted Stock Award is contingent on the
grantee executing the Restricted Stock Award Agreement. The terms and conditions
of each such Award Agreement shall be determined by the Administrator, and such
terms and conditions may differ among individual Awards and grantees.

        (b)    Rights as a Stockholder.    Upon execution of the Restricted
Stock Award Agreement and payment of any applicable purchase price, a grantee
shall have the rights of a stockholder with respect to the voting of the
Restricted Stock, subject to such conditions contained in the Restricted Stock
Award Agreement. Unless the Administrator shall otherwise determine,
(i) uncertificated Restricted Stock shall be accompanied by a notation on the
records of the Company or the transfer agent to the effect that they are subject
to forfeiture until such Restricted Stock are vested as provided in Section 7(d)
below, and (ii) certificated Restricted Stock shall remain in the possession of
the Company until such Restricted Stock is vested as provided in Section 7(d)
below, and the grantee shall be required, as a condition of the grant, to
deliver to the Company such instruments of transfer as the Administrator may
prescribe.

        (c)    Restrictions.    Restricted Stock may not be sold, assigned,
transferred, pledged or otherwise encumbered or disposed of except as
specifically provided herein or in the Restricted Stock Award Agreement. Except
as may otherwise be provided by the Administrator either in the Award Agreement
or, subject to Section 16 below, in writing after the Award Agreement is issued,
if any, if a grantee's

8

--------------------------------------------------------------------------------

employment (or other service relationship) with the Company and its Subsidiaries
terminates for any reason, any Restricted Stock that has not vested at the time
of termination shall automatically and without any requirement of notice to such
grantee from or other action by or on behalf of, the Company be deemed to have
been reacquired by the Company at its original purchase price (if any) from such
grantee or such grantee's legal representative simultaneously with such
termination of employment (or other service relationship), and thereafter shall
cease to represent any ownership of the Company by the grantee or rights of the
grantee as a stockholder. Following such deemed reacquisition of unvested
Restricted Stock that are represented by physical certificates, a grantee shall
surrender such certificates to the Company upon request without consideration.

        (d)    Vesting of Restricted Stock.    The Administrator at the time of
grant shall specify the date or dates and/or the attainment of pre-established
performance goals, objectives and other conditions on which the
non-transferability of the Restricted Stock and the Company's right of
repurchase or forfeiture shall lapse. Subsequent to such date or dates and/or
the attainment of such pre-established performance goals, objectives and other
conditions, the shares on which all restrictions have lapsed shall no longer be
Restricted Stock and shall be deemed "vested." Except as may otherwise be
provided by the Administrator either in the Award Agreement or, subject to
Section 16 below, in writing after the Award Agreement is issued, a grantee's
rights in any shares of Restricted Stock that have not vested shall
automatically terminate upon the grantee's termination of employment (or other
service relationship) with the Company and its Subsidiaries and such shares
shall be subject to the provisions of Section 7(c) above.

SECTION 8.    DEFERRED STOCK AWARDS

        (a)    Nature of Deferred Stock Awards.    The Administrator shall
determine the restrictions and conditions applicable to each Deferred Stock
Award at the time of grant. Conditions may be based on continuing employment (or
other service relationship) and/or achievement of pre-established performance
goals and objectives. The grant of a Deferred Stock Award is contingent on the
grantee executing the Deferred Stock Award Agreement. The terms and conditions
of each such Award Agreement shall be determined by the Administrator, and such
terms and conditions may differ among individual Awards and grantees. At the end
of the deferral period, the Deferred Stock Award, to the extent vested, shall be
settled in the form of shares of Stock.

        (b)    Election to Receive Deferred Stock Awards in Lieu of
Compensation.    The Administrator may, in its sole discretion, permit a grantee
to elect to receive a portion of future cash compensation otherwise due to such
grantee in the form of a Deferred Stock Award. Any such election shall be made
in writing and shall be delivered to the Company no later than the date
specified by the Administrator and in accordance with Section 409A and such
other rules and procedures established by the Administrator. Any such future
cash compensation that the grantee elects to defer shall be converted to a fixed
number of phantom stock units based on the Fair Market Value of Stock on the
date the compensation would otherwise have been paid to the grantee if such
payment had not been deferred as provided herein. The Administrator shall have
the sole right to determine whether and under what circumstances to permit such
elections and to impose such limitations and other terms and conditions thereon
as the Administrator deems appropriate.

        (c)    Rights as a Stockholder.    A grantee shall have the rights as a
stockholder only as to shares of Stock acquired by the grantee upon settlement
of a Deferred Stock Award; provided, however, that the grantee may be credited
with Dividend Equivalent Rights with respect to the phantom stock units
underlying his Deferred Stock Award, subject to such terms and conditions as the
Administrator may determine.

        (d)    Termination.    Except as may otherwise be provided by the
Administrator either in the Award Agreement or, subject to Section 16 below, in
writing after the Award Agreement is issued, a grantee's

9

--------------------------------------------------------------------------------

right in all Deferred Stock Awards that have not vested shall automatically
terminate upon the grantee's termination of employment (or cessation of service
relationship) with the Company and its Subsidiaries for any reason.

SECTION 9.    UNRESTRICTED STOCK AWARDS

         Grant or Sale of Unrestricted Stock.    The Administrator may, in its
sole discretion, grant (or sell at par value or such higher purchase price
determined by the Administrator) an Unrestricted Stock Award under the Plan.
Unrestricted Stock Awards may be granted in respect of past services or other
valid consideration, or in lieu of cash compensation due to such grantee.

SECTION 10.    CASH-BASED AWARDS

         Grant of Cash-based Awards.    The Administrator may, in its sole
discretion, grant Cash-based Awards to any grantee in such number or amount and
upon such terms, and subject to such conditions, as the Administrator shall
determine at the time of grant. The Administrator shall determine the maximum
duration of the Cash-based Award, the amount of cash to which the Cash-based
Award pertains, the conditions upon which the Cash-based Award shall become
vested or payable, and such other provisions as the Administrator shall
determine. Each Cash-based Award shall specify a cash-denominated payment
amount, formula or payment ranges as determined by the Administrator. Payment,
if any, with respect to a Cash-based Award shall be made in accordance with the
terms of the Award and may be made in cash or in shares of Stock, as the
Administrator determines.

SECTION 11.    DIVIDEND EQUIVALENT RIGHTS

        (a)    Dividend Equivalent Rights.    A Dividend Equivalent Right may be
granted hereunder to any grantee as a component of another Award or as a
freestanding award. The terms and conditions of Dividend Equivalent Rights shall
be specified in the Award Agreement. Dividend equivalents credited to the holder
of a Dividend Equivalent Right may be paid currently or may be deemed to be
reinvested in additional shares of Stock, which may thereafter accrue additional
equivalents. Any such reinvestment shall be at Fair Market Value on the date of
reinvestment or such other price as may then apply under a dividend reinvestment
plan sponsored by the Company, if any. Dividend Equivalent Rights may be settled
in cash or shares of Stock or a combination thereof, in a single installment or
installments. A Dividend Equivalent Right granted as a component of another
Award may provide that such Dividend Equivalent Right shall be settled upon
exercise, settlement, or payment of, or lapse of restrictions on, such other
Award, and that such Dividend Equivalent Right shall expire or be forfeited or
annulled under the same conditions as such other Award. A Dividend Equivalent
Right granted as a component of another Award may also contain terms and
conditions different from such other Award.

        (b)    Interest Equivalents.    Any Award under this Plan that is
settled in whole or in part in cash on a deferred basis may provide in the grant
for interest equivalents to be credited with respect to such cash payment.
Interest equivalents may be compounded and shall be paid upon such terms and
conditions as may be specified by the grant.

        (c)    Termination.    Except as may otherwise be provided by the
Administrator either in the Award Agreement or, subject to Section 16 below, in
writing after the Award Agreement is issued, a grantee's rights in all Dividend
Equivalent Rights or interest equivalents granted as a component of another
Award that has not vested shall automatically terminate upon the grantee's
termination of employment (or cessation of service relationship) with the
Company and its Subsidiaries for any reason.

10

--------------------------------------------------------------------------------

SECTION 12.    TRANSFERABILITY OF AWARDS

        (a)    Transferability.    Except as provided in Section 12(b) below,
during a grantee's lifetime, his or her Awards shall be exercisable only by the
grantee, or by the grantee's legal representative or guardian in the event of
the grantee's incapacity. No Awards shall be sold, assigned, transferred or
otherwise encumbered or disposed of by a grantee other than by will or by the
laws of descent and distribution. No Awards shall be subject, in whole or in
part, to attachment, execution, or levy of any kind, and any purported transfer
in violation hereof shall be null and void.

        (b)    Administrator Action.    Notwithstanding Section 12(a), the
Administrator, in its discretion, may provide either in the Award Agreement
regarding a given Award or by subsequent written approval that the grantee (who
is an employee or director) may transfer his or her Awards (other than any
Incentive Stock Options) to his or her immediate family members, to trusts for
the benefit of such family members, or to partnerships in which such family
members are the only partners, provided that the transferee agrees in writing
with the Company to be bound by all of the terms and conditions of this Plan and
the applicable Award.

        (c)    Family Member.    For purposes of Section 12(b), "family member"
shall mean a grantee's child, stepchild, grandchild, parent, stepparent,
grandparent, spouse, former spouse, sibling, niece, nephew, mother-in-law,
father-in-law, son-in-law, daughter-in-law, brother-in-law, or sister-in-law,
including adoptive relationships, any person sharing the grantee's household
(other than a tenant of the grantee), a trust in which these persons (or the
grantee) have more than 50 percent of the beneficial interest, a foundation in
which these persons (or the grantee) control the management of assets, and any
other entity in which these persons (or the grantee) own more than 50 percent of
the voting interests.

        (d)    Designation of Beneficiary.    Each grantee to whom an Award has
been made under the Plan may designate a beneficiary or beneficiaries to
exercise any Award or receive any payment under any Award payable on or after
the grantee's death. Any such designation shall be on a form provided for that
purpose by the Administrator and shall not be effective until received by the
Administrator. If no beneficiary has been designated by a deceased grantee, or
if the designated beneficiaries have predeceased the grantee, the beneficiary
shall be the grantee's estate.

SECTION 13.    TAX WITHHOLDING

        (a)    Payment by Grantee.    Each grantee shall, no later than the date
as of which the value of an Award or of any Stock or other amounts received
thereunder first becomes includable in the gross income of the grantee for
Federal income tax purposes, pay to the Company, or make arrangements
satisfactory to the Administrator regarding payment of, any Federal, state, or
local taxes of any kind required by law to be withheld by the Company with
respect to such income. The Company and its Subsidiaries shall, to the extent
permitted by law, have the right to deduct any such taxes from any payment of
any kind otherwise due to the grantee. The Company's obligation to deliver
evidence of book entry (or stock certificates) to any grantee is subject to and
conditioned on tax withholding obligations being satisfied by the grantee.

        (b)    Payment in Stock.    Subject to approval by the Administrator, a
grantee may elect to have the Company's minimum required tax withholding
obligation satisfied, in whole or in part, by authorizing the Company to
withhold from shares of Stock to be issued pursuant to any Award a number of
shares with an aggregate Fair Market Value (as of the date the withholding is
effected) that would satisfy the withholding amount due.

11

--------------------------------------------------------------------------------

SECTION 14.    ADDITIONAL CONDITIONS APPLICABLE TO NONQUALIFIED DEFERRED
COMPENSATION UNDER SECTION 409A.

        In the event any Stock Option or Stock Appreciation Right under the Plan
is materially modified and deemed a new grant at a time when the Fair Market
Value exceeds the exercise price, or any other Award is otherwise determined to
constitute "nonqualified deferred compensation" within the meaning of
Section 409A (a "409A Award"), the following additional conditions shall apply
and shall supersede any contrary provisions of this Plan or the terms of any
agreement relating to such 409A Award.

        (a)    Exercise and Distribution.    Except as provided in Section 14(b)
hereof, no 409A Award shall be exercisable or distributable earlier than upon
one of the following:

        (i)    Specified Time.    A specified time or a fixed schedule set forth
in the written instrument evidencing the 409A Award.

        (ii)    Separation from Service.    Separation from service (within the
meaning of Section 409A) by the 409A Award grantee; provided, however, that if
the 409A Award grantee is a "key employee" (as defined in Section 416(i) of the
Code without regard to paragraph (5) thereof) and any of the Company's Stock is
publicly traded on an established securities market or otherwise, exercise or
distribution under this Section 14(a)(ii) may not be made before the date that
is six months after the date of separation from service.

        (iii)    Death.    The date of death of the 409A Award grantee.

        (iv)    Disability.    The date the 409A Award grantee becomes disabled
(within the meaning of Section 14(c)(ii) hereof).

        (v)    Unforeseeable Emergency.    The occurrence of an unforeseeable
emergency (within the meaning of Section 14(c)(iii) hereof), but only if the net
value (after payment of the exercise price) of the number of shares of Stock
that become issuable does not exceed the amounts necessary to satisfy such
emergency plus amounts necessary to pay taxes reasonably anticipated as a result
of the exercise, after taking into account the extent to which the emergency is
or may be relieved through reimbursement or compensation by insurance or
otherwise or by liquidation of the grantee's other assets (to the extent such
liquidation would not itself cause severe financial hardship).

        (vi)    Change in Control Event.    The occurrence of a Change in
Control Event (within the meaning of Section 14(c)(i) hereof), including the
Company's discretionary exercise of the right to accelerate vesting of such
grant upon a Change in Control Event or to terminate the Plan or any 409A Award
granted hereunder within 12 months of the Change in Control Event.

        (b)    No Acceleration.    A 409A Award may not be accelerated or
exercised prior to the time specified in Section 14(a) hereof, except in the
case of one of the following events:

        (i)    Domestic Relations Order.    The 409A Award may permit the
acceleration of the exercise or distribution time or schedule to an individual
other than the grantee as may be necessary to comply with the terms of a
domestic relations order (as defined in Section 414(p)(1)(B) of the Code).

        (ii)    Conflicts of Interest.    The 409A Award may permit the
acceleration of the exercise or distribution time or schedule as may be
necessary to comply with the terms of a certificate of divestiture (as defined
in Section 1043(b)(2) of the Code).

        (iii)    Change in Control Event.    The Administrator may exercise the
discretionary right to accelerate the vesting of such 409A Award upon a Change
in Control Event or to terminate the Plan or any 409A Award granted thereunder
within 12 months of the Change in Control Event and cancel the 409A Award for
compensation.

12

--------------------------------------------------------------------------------

        (c)    Definitions.    Solely for purposes of this Section 14 and not
for other purposes of the Plan, the following terms shall be defined as set
forth below:

        (i)    "Change in Control Event" means the occurrence of a change in the
ownership of the Company, a change in effective control of the Company, or a
change in the ownership of a substantial portion of the assets of the Company
(as defined in Section 1.409A-3(g) of the proposed regulations promulgated under
Section 409A by the Department of the Treasury on September 29, 2005 or any
subsequent guidance).

        (ii)    "Disabled" means a grantee who (i) is unable to engage in any
substantial gainful activity by reason of any medically determinable physical or
mental impairment that can be expected to result in death or can be expected to
last for a continuous period of not less than 12 months, or (ii) is, by reason
of any medically determinable physical or mental impairment that can be expected
to result in death or can be expected to last for a continuous period of not
less than 12 months, receiving income replacement benefits for a period of not
less than three months under an accident and health plan covering employees of
the Company or its Subsidiaries.

        (iii)    "Unforeseeable Emergency" means a severe financial hardship to
the grantee resulting from an illness or accident of the grantee, the grantee's
spouse, or a dependent (as defined in Section 152(a) of the Code) of the
grantee, loss of the grantee's property due to casualty, or similar
extraordinary and unforeseeable circumstances arising as a result of events
beyond the control of the grantee.

SECTION 15.    TRANSFER, LEAVE OF ABSENCE, ETC.

        For purposes of the Plan, the following events shall not be deemed a
termination of employment:

        (a)   a transfer to the employment of the Company from a Subsidiary or
from the Company to a Subsidiary, or from one Subsidiary to another; or

        (b)   an approved leave of absence for military service or sickness, or
for any other purpose approved by the Company, if the employee's right to
re-employment is guaranteed either by a statute or by contract or under the
policy pursuant to which the leave of absence was granted or if the
Administrator otherwise so provides in writing.

SECTION 16.    AMENDMENTS AND TERMINATION

        The Board may, at any time, amend or discontinue the Plan and the
Administrator may, at any time, amend or cancel any outstanding Award for the
purpose of satisfying changes in law or for any other lawful purpose, but no
such action shall adversely affect rights under any outstanding Award without
the holder's consent. Except as provided in Section 3(b) or 3(c), in no event
may the Administrator exercise its discretion to reduce the exercise price of
outstanding Stock Options or Stock Appreciation Rights or effect repricing
through cancellation and re-grants. Any material Plan amendments (other than
amendments that curtail the scope of the Plan), including any Plan amendments
that (i) increase the number of shares reserved for issuance under the Plan,
(ii) expand the type of Awards available under, materially expand the
eligibility to participate in, or materially extend the term of, the Plan, or
(iii) materially change the method of determining Fair Market Value, shall be
subject to approval by the Company stockholders entitled to vote at a meeting of
stockholders. In addition, to the extent determined by the Administrator to be
required by the Code to ensure that Incentive Stock Options granted under the
Plan are qualified under Section 422 of the Code or to ensure that compensation
earned under Awards qualifies as performance-based compensation under
Section 162(m) of the Code, Plan amendments shall be subject to approval by the
Company stockholders entitled to vote at a meeting of stockholders. Nothing in
this Section 16 shall limit the Administrator's authority to take any action
permitted pursuant to Section 3(c).

13

--------------------------------------------------------------------------------

SECTION 17.    STATUS OF PLAN

        With respect to the portion of any Award that has not been exercised and
any payments in cash, Stock or other consideration not received by a grantee, a
grantee shall have no rights greater than those of a general creditor of the
Company unless the Administrator shall otherwise expressly determine in
connection with any Award or Awards. In its sole discretion, the Administrator
may authorize the creation of trusts or other arrangements to meet the Company's
obligations to deliver Stock or make payments with respect to Awards hereunder,
provided that the existence of such trusts or other arrangements is consistent
with the foregoing sentence.

SECTION 18.    GENERAL PROVISIONS

        (a)    No Distribution.    The Administrator may require each person
acquiring Stock pursuant to an Award to represent to and agree with the Company
in writing that such person is acquiring the shares without a view to
distribution thereof.

        (b)    Delivery of Stock Certificates.    Stock certificates to grantees
under this Plan shall be deemed delivered for all purposes when the Company or a
stock transfer agent of the Company shall have mailed such certificates in the
United States mail, addressed to the grantee, at the grantee's last known
address on file with the Company. Uncertificated Stock shall be deemed delivered
for all purposes when the Company or a Stock transfer agent of the Company shall
have given to the grantee by electronic mail (with proof of receipt) or by
United States mail, addressed to the grantee, at the grantee's last known
address on file with the Company, notice of issuance and recorded the issuance
in its records (which may include electronic "book entry" records).
Notwithstanding anything herein to the contrary, the Company shall not be
required to issue or deliver any certificates evidencing shares of Stock
pursuant to the exercise of any Award, unless and until the Board has
determined, with advice of counsel (to the extent the Board deems such advice
necessary or advisable), that the issuance and delivery of such certificates is
in compliance with all applicable laws, regulations of governmental authorities
and, if applicable, the requirements of any exchange on which the shares of
Stock are listed, quoted or traded. All Stock certificates delivered pursuant to
the Plan shall be subject to any stop-transfer orders and other restrictions as
the Administrator deems necessary or advisable to comply with federal, state or
foreign jurisdiction, securities or other laws, rules and quotation system on
which the Stock is listed, quoted or traded. The Administrator may place legends
on any Stock certificate to reference restrictions applicable to the Stock. In
addition to the terms and conditions provided herein, the Board may require that
an individual make such reasonable covenants, agreements, and representations as
the Board, in its discretion, deems necessary or advisable in order to comply
with any such laws, regulations, or requirements. The Administrator shall have
the right to require any individual to comply with any timing or other
restrictions with respect to the settlement or exercise of any Award, including
a window-period limitation, as may be imposed in the discretion of the
Administrator.

        (c)    Stockholder Rights.    Until Stock is deemed delivered in
accordance with Section 18(b), no right to vote or receive dividends or any
other rights of a stockholder will exist with respect to shares of Stock to be
issued in connection with an Award, notwithstanding the exercise of a Stock
Option or any other action by the grantee with respect to an Award.

        (d)    Other Compensation Arrangements; No Employment Rights.    Nothing
contained in this Plan shall prevent the Board from adopting other or additional
compensation arrangements, including trusts, and such arrangements may be either
generally applicable or applicable only in specific cases. The adoption of this
Plan and the grant of Awards do not confer upon any employee any right to
continued employment with the Company or any Subsidiary.

14

--------------------------------------------------------------------------------

        (e)    Trading Policy Restrictions.    Option exercises and other Awards
under the Plan shall be subject to such Company's insider trading policy and
procedures, as in effect from time to time.

        (f)    Forfeiture of Awards under Sarbanes-Oxley Act.    If the Company
is required to prepare an accounting restatement due to the material
noncompliance of the Company, as a result of misconduct, with any financial
reporting requirement under the securities laws, then any grantee who is one of
the individuals subject to automatic forfeiture under Section 304 of the
Sarbanes-Oxley Act of 2002 shall reimburse the Company for the amount of any
Award received by such individual under the Plan during the 12-month period
following the first public issuance or filing with the United States Securities
and Exchange Commission, as the case may be, of the financial document embodying
such financial reporting requirement.

SECTION 19.    EFFECTIVE DATE OF PLAN

        This Plan shall become effective upon approval by the holders of a
majority of the votes cast at a meeting of stockholders at which a quorum is
present or pursuant to written consent. No grants of Stock Options and other
Awards may be made hereunder after the tenth anniversary of the Effective Date
and no grants of Incentive Stock Options may be made hereunder after the tenth
anniversary of the date the Plan is approved by the Board.

SECTION 20.    GOVERNING LAW

        This Plan and all Awards and actions taken thereunder shall be governed
by, and construed in accordance with, the laws of Delaware, applied without
regard to conflict of law principles.

DATE APPROVED BY BOARD OF DIRECTORS: ______________, 2007

DATE APPROVED BY STOCKHOLDERS: ______________, 2007

15

--------------------------------------------------------------------------------

INCENTIVE STOCK OPTION AGREEMENT
UNDER THE HELICOS BIOSCIENCES CORPORATION
2007 STOCK OPTION AND INCENTIVE PLAN

Name of Optionee:  

--------------------------------------------------------------------------------

      No. of Option Shares:  

--------------------------------------------------------------------------------

      Option Exercise Price per Share: $  

--------------------------------------------------------------------------------

     
[FMV on Grant Date (110% of FMV if a 10% owner)]
 
 
Grant Date:
 

--------------------------------------------------------------------------------

 
 
  Vesting Start Date:  

--------------------------------------------------------------------------------

      Expiration Date: Ten Years from Grant Date [5 years if 10% owner]    

        Pursuant to the Helicos BioSciences Corporation 2007 Stock Option and
Incentive Plan as amended through the date hereof (the "Plan"), Helicos
BioSciences Corporation (the "Company") hereby grants to the Optionee named
above an option (the "Stock Option") to purchase on or prior to the Expiration
Date specified above all or part of the number of shares of Common Stock, par
value $0.001 per share (the "Stock"), of the Company specified above at the
Option Exercise Price per Share specified above subject to the terms and
conditions set forth herein and in the Plan.

        1.    Exercisability Schedule.    No portion of this Stock Option may be
exercised until such portion shall have become exercisable. Except as set forth
below, and subject to the discretion of the Administrator (as defined in
Section 2 of the Plan) to accelerate the exercisability schedule hereunder, this
Stock Option shall be exercisable with respect to the following number of Option
Shares on the dates indicated:

Incremental Number of
Option Shares Exercisable   Exercisability Date 25% of Shares   One year from
Vesting Start Date An additional 2.0833333% of the Shares   The first day of
each month following the first anniversary of the Vesting Start Date.

[Note that for ISOs, Option Shares for no more than
$100,000 may become exercisable per year.]

        Once exercisable, this Stock Option shall continue to be exercisable at
any time or times prior to the close of business on the Expiration Date, subject
to the provisions hereof and of the Plan.

        2.    Manner of Exercise.    

        (a)    The Optionee may exercise this Stock Option only in the following
manner: from time to time on or prior to the Expiration Date of this Stock
Option, the Optionee may give written notice to the Administrator of his or her
election to purchase some or all of the Option Shares purchasable at the time of
such notice. This notice shall specify the number of Option Shares to be
purchased.

        Payment of the purchase price for the Option Shares may be made by one
or more of the following methods: (i) in cash, by certified or bank check or
other instrument acceptable to the Administrator; (ii) through the delivery (or
attestation to the ownership) of shares of Stock that have been purchased by the
Optionee on the open market or that are beneficially owned by the Optionee and
are not then subject to any restrictions under any Company plan and that
otherwise satisfy any holding periods as may be required by the Administrator;
(iii) by the Optionee delivering to the Company a properly executed exercise
notice together with irrevocable instructions to a broker to promptly deliver to
the Company cash or a check payable and acceptable to the Company to pay the
option purchase price, provided that in the event the Optionee chooses to pay
the option purchase price as so provided, the Optionee and the broker shall
comply with such procedures and enter into

--------------------------------------------------------------------------------

such agreements of indemnity and other agreements as the Administrator shall
prescribe as a condition of such payment procedure; or (iv) a combination of
(i), (ii) and (iii) above. Payment instruments will be received subject to
collection.

        The transfer to the Optionee on the records of the Company or of the
transfer agent of the Option Shares will be contingent upon (i) the Company's
receipt from the Optionee of the full purchase price for the Option Shares, as
set forth above, (ii) the fulfillment of any other requirements contained herein
or in the Plan or in any other agreement or provision of laws, and (iii) the
receipt by the Company of any agreement, statement or other evidence that the
Company may require to satisfy itself that the issuance of Stock to be purchased
pursuant to the exercise of Stock Options under the Plan and any subsequent
resale of the shares of Stock will be in compliance with applicable laws and
regulations. In the event the Optionee chooses to pay the purchase price by
previously-owned shares of Stock through the attestation method, the number of
shares of Stock transferred to the Optionee upon the exercise of the Stock
Option shall be net of the shares attested to.

        (b)    The shares of Stock purchased upon exercise of this Stock Option
shall be transferred to the Optionee on the records of the Company or of the
transfer agent upon compliance to the satisfaction of the Administrator with all
requirements under applicable laws or regulations in connection with such
issuance and with the requirements hereof and of the Plan. The determination of
the Administrator as to such compliance shall be final and binding on the
Optionee. The Optionee shall not be deemed to be the holder of, or to have any
of the rights of a holder with respect to, any shares of Stock subject to this
Stock Option unless and until this Stock Option shall have been exercised
pursuant to the terms hereof, the Company or the transfer agent shall have
transferred the shares to the Optionee, and the Optionee's name shall have been
entered as the stockholder of record on the books of the Company. Thereupon, the
Optionee shall have full voting, dividend and other ownership rights with
respect to such shares of Stock.

        (c)    The minimum number of shares with respect to which this Stock
Option may be exercised at any one time shall be 100 shares, unless the number
of shares with respect to which this Stock Option is being exercised is the
total number of shares subject to exercise under this Stock Option at the time.

        (d)    Notwithstanding any other provision hereof or of the Plan, no
portion of this Stock Option shall be exercisable after the Expiration Date
hereof.

        3.    Termination of Employment.    If the Optionee's employment by the
Company or a Subsidiary (as defined in the Plan) is terminated, the period
within which to exercise the Stock Option may be subject to earlier termination
as set forth below.

        (a)    Termination Due to Death.    If the Optionee's employment
terminates by reason of the Optionee's death, any portion of this Stock Option
outstanding on such date shall become fully exercisable and may thereafter be
exercised by the Optionee's legal representative or legatee for a period of
12 months from the date of death or until the Expiration Date, if earlier.

        (b)    Termination Due to Disability.    If the Optionee's employment
terminates by reason of the Optionee's disability (as determined by the
Administrator), any portion of this Stock Option outstanding on such date shall
become fully exercisable and may thereafter be exercised by the Optionee for a
period of 12 months from the date of termination or until the Expiration Date,
if earlier.

        (c)    Termination for Cause.    If the Optionee's employment terminates
for Cause, any portion of this Stock Option outstanding on such date shall
terminate immediately and be of no further force and effect. For purposes
hereof, "Cause" shall mean, unless otherwise provided in an employment agreement
between the Company and the Optionee, a determination by the Administrator that
the Optionee shall be dismissed as a result of (i) any material breach by the
Optionee of any agreement between the Optionee and the Company; (ii) the
conviction of, indictment for or plea of nolo

2

--------------------------------------------------------------------------------

contendere by the Optionee to a felony or a crime involving moral turpitude; or
(iii) any material misconduct or willful and deliberate non-performance (other
than by reason of disability) by the Optionee of the Optionee's duties to the
Company.

        (d)    Other Termination.    If the Optionee's employment terminates for
any reason other than the Optionee's death, the Optionee's disability, or Cause,
and unless otherwise determined by the Administrator, any portion of this Stock
Option outstanding on such date may be exercised, to the extent exercisable on
the date of termination, for a period of three months from the date of
termination or until the Expiration Date, if earlier. Any portion of this Stock
Option that is not exercisable on the date of termination shall terminate
immediately and be of no further force or effect.

        The Administrator's determination of the reason for termination of the
Optionee's employment shall be conclusive and binding on the Optionee and his or
her representatives or legatees.

        4.    Incorporation of Plan.    Notwithstanding anything herein to the
contrary, this Stock Option shall be subject to and governed by all the terms
and conditions of the Plan, including the powers of the Administrator set forth
in Section 2(b) of the Plan. Capitalized terms in this Agreement shall have the
meaning specified in the Plan, unless a different meaning is specified herein.

        5.    Transferability.    This Agreement is personal to the Optionee, is
non-assignable and is not transferable in any manner, by operation of law or
otherwise, other than by will or the laws of descent and distribution. This
Stock Option is exercisable, during the Optionee's lifetime, only by the
Optionee, and thereafter, only by the Optionee's legal representative or
legatee.

        6.    Status of the Stock Option.    This Stock Option is intended to
qualify as an "incentive stock option" under Section 422 of the Internal Revenue
Code of 1986, as amended (the "Code"), but the Company does not represent or
warrant that this Stock Option qualifies as such. The Optionee should consult
with his or her own tax advisors regarding the tax effects of this Stock Option
and the requirements necessary to obtain favorable income tax treatment under
Section 422 of the Code, including, but not limited to, holding period
requirements. To the extent any portion of this Stock Option does not so qualify
as an "incentive stock option," such portion shall be deemed to be a
non-qualified stock option. If the Optionee intends to dispose or does dispose
(whether by sale, gift, transfer or otherwise) of any Option Shares within the
one-year period beginning on the date after the transfer of such shares to him
or her, or within the two-year period beginning on the day after the grant of
this Stock Option, he or she will so notify the Company within 30 days after
such disposition.

        7.    Tax Withholding.    The Optionee shall, not later than the date as
of which the exercise of this Stock Option becomes a taxable event for Federal
income tax purposes, pay to the Company or make arrangements satisfactory to the
Administrator for payment of any Federal, state, and local taxes required by law
to be withheld on account of such taxable event. The Optionee may elect to have
the minimum required tax withholding obligation satisfied, in whole or in part,
by authorizing the Company to withhold from shares of Stock to be issued a
number of shares of Stock with an aggregate Fair Market Value that would satisfy
the withholding amount due.

        8.    No Obligation to Continue Employment.    Neither the Company nor
any Subsidiary is obligated by or as a result of the Plan or this Agreement to
continue the Optionee in employment and neither the Plan nor this Agreement
shall interfere in any way with the right of the Company or any Subsidiary to
terminate the employment of the Optionee at any time.

        9.    Notices.    Notices hereunder shall be mailed or delivered to the
Company at its principal place of business and shall be mailed or delivered to
the Optionee at the address on file with the Company

3

--------------------------------------------------------------------------------

or, in either case, at such other address as one party may subsequently furnish
to the other party in writing.

        HELICOS BIOSCIENCES CORPORATION
 
 
 
 
By:
 
             

--------------------------------------------------------------------------------

Title:

        The foregoing Agreement is hereby accepted and the terms and conditions
thereof hereby agreed to by the undersigned.

Dated:                

--------------------------------------------------------------------------------

   

--------------------------------------------------------------------------------

Optionee's Signature
 
 
 
 
Optionee's name and address:
 
 
 
 

--------------------------------------------------------------------------------

         

--------------------------------------------------------------------------------

         

--------------------------------------------------------------------------------

4

--------------------------------------------------------------------------------

NON-QUALIFIED STOCK OPTION AGREEMENT FOR COMPANY EMPLOYEES
UNDER THE HELICOS BIOSCIENCES CORPORATION
2007 STOCK OPTION AND INCENTIVE PLAN

Name of Optionee:  

--------------------------------------------------------------------------------

      No. of Option Shares:  

--------------------------------------------------------------------------------

      Option Exercise Price per Share: $  

--------------------------------------------------------------------------------

     
[FMV on Grant Date
 
 
Grant Date:
 

--------------------------------------------------------------------------------

 
 
  Vesting Start Date:  

--------------------------------------------------------------------------------

      Expiration Date: Ten Years from Grant Date    

        Pursuant to the Helicos Biosciences Corporation 2007 Stock Option and
Incentive Plan as amended through the date hereof (the "Plan"), Helicos
Biosciences Corporation (the "Company") hereby grants to the Optionee named
above an option (the "Stock Option") to purchase on or prior to the Expiration
Date specified above all or part of the number of shares of Common Stock, par
value $0.001 per share (the "Stock") of the Company specified above at the
Option Exercise Price per Share specified above subject to the terms and
conditions set forth herein and in the Plan. This Stock Option is not intended
to be an "incentive stock option" under Section 422 of the Internal Revenue Code
of 1986, as amended.

        1.    Exercisability Schedule.    No portion of this Stock Option may be
exercised until such portion shall have become exercisable. Except as set forth
below, and subject to the discretion of the Administrator (as defined in
Section 2 of the Plan) to accelerate the exercisability schedule hereunder, this
Stock Option shall be exercisable with respect to the following number of Option
Shares on the dates indicated:

Incremental Number of
Option Shares Exercisable   Exercisability Date 25% of Shares   One year from
Vesting Start Date An additional 2.0833333% of the Shares   The first day of
each month following the first anniversary of the Vesting Start Date.

        Once exercisable, this Stock Option shall continue to be exercisable at
any time or times prior to the close of business on the Expiration Date, subject
to the provisions hereof and of the Plan.

        2.    Manner of Exercise.    

        (a)    The Optionee may exercise this Stock Option only in the following
manner: from time to time on or prior to the Expiration Date of this Stock
Option, the Optionee may give written notice to the Administrator of his or her
election to purchase some or all of the Option Shares purchasable at the time of
such notice. This notice shall specify the number of Option Shares to be
purchased.

        Payment of the purchase price for the Option Shares may be made by one
or more of the following methods: (i) in cash, by certified or bank check or
other instrument acceptable to the Administrator; (ii) through the delivery (or
attestation to the ownership) of shares of Stock that have been purchased by the
Optionee on the open market or that are beneficially owned by the Optionee and
are not then subject to any restrictions under any Company plan and that
otherwise satisfy any holding periods as may be required by the Administrator;
(iii) by the Optionee delivering to the Company a properly executed exercise
notice together with irrevocable instructions to a broker to promptly deliver to
the Company cash or a check payable and acceptable to the Company to pay the
option purchase price, provided that in the event the Optionee chooses to pay
the option purchase price as so provided, the Optionee and the broker shall
comply with such procedures and enter into such agreements of indemnity and
other agreements as the Administrator shall prescribe as a condition

--------------------------------------------------------------------------------

of such payment procedure; or (iv) a combination of (i), (ii) and (iii) above.
Payment instruments will be received subject to collection.

        The transfer to the Optionee on the records of the Company or of the
transfer agent of the Option Shares will be contingent upon (i) the Company's
receipt from the Optionee of the full purchase price for the Option Shares, as
set forth above, (ii) the fulfillment of any other requirements contained herein
or in the Plan or in any other agreement or provision of laws, and (iii) the
receipt by the Company of any agreement, statement or other evidence that the
Company may require to satisfy itself that the issuance of Stock to be purchased
pursuant to the exercise of Stock Options under the Plan and any subsequent
resale of the shares of Stock will be in compliance with applicable laws and
regulations. In the event the Optionee chooses to pay the purchase price by
previously-owned shares of Stock through the attestation method, the number of
shares of Stock transferred to the Optionee upon the exercise of the Stock
Option shall be net of the Shares attested to.

        (b)    The shares of Stock purchased upon exercise of this Stock Option
shall be transferred to the Optionee on the records of the Company or of the
transfer agent upon compliance to the satisfaction of the Administrator with all
requirements under applicable laws or regulations in connection with such
issuance and with the requirements hereof and of the Plan. The determination of
the Administrator as to such compliance shall be final and binding on the
Optionee. The Optionee shall not be deemed to be the holder of, or to have any
of the rights of a holder with respect to, any shares of Stock subject to this
Stock Option unless and until this Stock Option shall have been exercised
pursuant to the terms hereof, the Company or the transfer agent shall have
transferred the shares to the Optionee, and the Optionee's name shall have been
entered as the stockholder of record on the books of the Company. Thereupon, the
Optionee shall have full voting, dividend and other ownership rights with
respect to such shares of Stock.

        (c)    The minimum number of shares with respect to which this Stock
Option may be exercised at any one time shall be 100 shares, unless the number
of shares with respect to which this Stock Option is being exercised is the
total number of shares subject to exercise under this Stock Option at the time.

        (d)    Notwithstanding any other provision hereof or of the Plan, no
portion of this Stock Option shall be exercisable after the Expiration Date
hereof.

        3.    Termination of Employment.    If the Optionee's employment by the
Company or a Subsidiary (as defined in the Plan) is terminated, the period
within which to exercise the Stock Option may be subject to earlier termination
as set forth below.

        (a)    Termination Due to Death.    If the Optionee's employment
terminates by reason of the Optionee's death, any portion of this Stock Option
outstanding on such date shall become fully exercisable and may thereafter be
exercised by the Optionee's legal representative or legatee for a period of
12 months from the date of death or until the Expiration Date, if earlier.

        (b)    Termination Due to Disability.    If the Optionee's employment
terminates by reason of the Optionee's disability (as determined by the
Administrator), any portion of this Stock Option outstanding on such date shall
become fully exercisable and may thereafter be exercised by the Optionee for a
period of 12 months from the date of termination or until the Expiration Date,
if earlier.

        (c)    Termination for Cause.    If the Optionee's employment terminates
for Cause, any portion of this Stock Option outstanding on such date shall
terminate immediately and be of no further force and effect. For purposes
hereof, "Cause" shall mean, unless otherwise provided in an employment agreement
between the Company and the Optionee, a determination by the Administrator that
the Optionee shall be dismissed as a result of (i) any material breach by the
Optionee of any agreement between the Optionee and the Company; (ii) the
conviction of, indictment for or plea of nolo contendere by the Optionee to a
felony or a crime involving moral turpitude; or (iii) any material

2

--------------------------------------------------------------------------------

misconduct or willful and deliberate non-performance (other than by reason of
disability) by the Optionee of the Optionee's duties to the Company.

        (d)    Other Termination.    If the Optionee's employment terminates for
any reason other than the Optionee's death, the Optionee's disability or Cause,
and unless otherwise determined by the Administrator, any portion of this Stock
Option outstanding on such date may be exercised, to the extent exercisable on
the date of termination, for a period of three months from the date of
termination or until the Expiration Date, if earlier. Any portion of this Stock
Option that is not exercisable on the date of termination shall terminate
immediately and be of no further force or effect.

        The Administrator's determination of the reason for termination of the
Optionee's employment shall be conclusive and binding on the Optionee and his or
her representatives or legatees.

        4.    Incorporation of Plan.    Notwithstanding anything herein to the
contrary, this Stock Option shall be subject to and governed by all the terms
and conditions of the Plan, including the powers of the Administrator set forth
in Section 2(b) of the Plan. Capitalized terms in this Agreement shall have the
meaning specified in the Plan, unless a different meaning is specified herein.

        5.    Transferability.    This Agreement is personal to the Optionee, is
non-assignable and is not transferable in any manner, by operation of law or
otherwise, other than by will or the laws of descent and distribution. This
Stock Option is exercisable, during the Optionee's lifetime, only by the
Optionee, and thereafter, only by the Optionee's legal representative or
legatee.

        6.    Tax Withholding.    The Optionee shall, not later than the date as
of which the exercise of this Stock Option becomes a taxable event for Federal
income tax purposes, pay to the Company or make arrangements satisfactory to the
Administrator for payment of any Federal, state, and local taxes required by law
to be withheld on account of such taxable event. The Optionee may elect to have
the minimum required tax withholding obligation satisfied, in whole or in part,
by authorizing the Company to withhold from shares of Stock to be issued a
number of shares of Stock with an aggregate Fair Market Value that would satisfy
the withholding amount due.

        7.    No Obligation to Continue Employment.    Neither the Company nor
any Subsidiary is obligated by or as a result of the Plan or this Agreement to
continue the Optionee in employment and neither the Plan nor this Agreement
shall interfere in any way with the right of the Company or any Subsidiary to
terminate the employment of the Optionee at any time.

        8.    Notices.    Notices hereunder shall be mailed or delivered to the
Company at its principal place of business and shall be mailed or delivered to
the Optionee at the address on file with the Company or, in either case, at such
other address as one party may subsequently furnish to the other party in
writing.

        HELICOS BIOSCIENCES CORPORATION
 
 
 
 
By:
 
             

--------------------------------------------------------------------------------

Title:

3

--------------------------------------------------------------------------------

        The foregoing Agreement is hereby accepted and the terms and conditions
thereof hereby agreed to by the undersigned.

Dated:                

--------------------------------------------------------------------------------

   

--------------------------------------------------------------------------------

Optionee's Signature
 
 
 
 
Optionee's name and address:
 
 
 
 

--------------------------------------------------------------------------------

         

--------------------------------------------------------------------------------

         

--------------------------------------------------------------------------------

4

--------------------------------------------------------------------------------

RESTRICTED STOCK AWARD AGREEMENT
UNDER THE HELICOS BIOSCIENCES CORPORATION
2007 STOCK OPTION AND INCENTIVE PLAN

Name of Grantee:  

--------------------------------------------------------------------------------

      No. of Shares:  

--------------------------------------------------------------------------------

      Grant Date:  

--------------------------------------------------------------------------------

      Vesting Start Date:  

--------------------------------------------------------------------------------

      Final Acceptance Date:  

--------------------------------------------------------------------------------

     

        Pursuant to the Helicos BioSciences Corporation 2007 Stock Option and
Incentive Plan (the "Plan") as amended through the date hereof, Helicos
BioSciences Corporation (the "Company") hereby grants a Restricted Stock Award
(an "Award") to the Grantee named above. Upon acceptance of this Award, the
Grantee shall receive the number of shares of Common Stock, par value $0.001 per
share (the "Stock") of the Company specified above, subject to the restrictions
and conditions set forth herein and in the Plan. The Company acknowledges the
receipt from the Grantee of consideration with respect to the par value of the
Stock in the form of cash, past or future services rendered to the Company by
the Grantee or such other form of consideration as is acceptable to the
Administrator.

        1.    Acceptance of Award.    The Grantee shall have no rights with
respect to this Award unless he or she shall have accepted this Award prior to
the close of business on the Final Acceptance Date specified above by
(i) signing and delivering to the Company a copy of this Award Agreement, and
(ii) delivering to the Company a stock power endorsed in blank. Upon acceptance
of this Award by the Grantee, the shares of Restricted Stock so accepted shall
be issued and held by the Company's transfer agent in book entry form, and the
Grantee's name shall be entered as the stockholder of record on the books of the
Company. Thereupon, the Grantee shall have all the rights of a stockholder with
respect to such shares, including voting and dividend rights, subject, however,
to the restrictions and conditions specified in Paragraph 2 below.

        2.    Restrictions and Conditions.    

        (a)    Any book entries for the shares of Restricted Stock granted
herein shall bear an appropriate legend, as determined by the Administrator in
its sole discretion, to the effect that such shares are subject to restrictions
as set forth herein and in the Plan.

        (b)    Shares of Restricted Stock granted herein may not be sold,
assigned, transferred, pledged or otherwise encumbered or disposed of by the
Grantee prior to vesting.

        (c)    If the Grantee's employment with the Company and its Subsidiaries
is voluntarily or involuntarily terminated for any reason (including death)
prior to vesting of shares of Restricted Stock granted herein, all unvested
shares of Restricted Stock shall immediately and automatically be forfeited and
returned to the Company.

        3.    Vesting of Restricted Stock.    The restrictions and conditions in
Paragraph 2 of this Agreement shall lapse on the Vesting Date or Dates specified
in the following schedule so long as the Grantee remains an employee of the
Company or a Subsidiary on such Dates. If a series of Vesting Dates is
specified, then the restrictions and conditions in Paragraph 2 shall lapse only
with respect to the number of shares of Restricted Stock specified as vested on
such date.

Shares Vested
Number of   Vesting Date 25% of Shares
An additional 2.0833333% of the Shares   One year from Vesting Start Date
The first day of each month following the first anniversary of the Vesting Start
Date.

--------------------------------------------------------------------------------

        Subsequent to such Vesting Date or Dates, the shares of Stock on which
all restrictions and conditions have lapsed shall no longer be deemed Restricted
Stock. The Administrator may at any time accelerate the vesting schedule
specified in this Paragraph 3.

        4.    Dividends.    Dividends on Shares of Restricted Stock shall be
paid currently to the Grantee.

        5.    Incorporation of Plan.    Notwithstanding anything herein to the
contrary, this Agreement shall be subject to and governed by all the terms and
conditions of the Plan, including the powers of the Administrator set forth in
Section 2(b) of the Plan. Capitalized terms in this Agreement shall have the
meaning specified in the Plan, unless a different meaning is specified herein.

        6.    Transferability.    This Agreement is personal to the Grantee, is
non-assignable and is not transferable in any manner, by operation of law or
otherwise, other than by will or the laws of descent and distribution.

        7.    Tax Withholding.    The Grantee shall, not later than the date as
of which the receipt of this Award becomes a taxable event for Federal income
tax purposes, pay to the Company or make arrangements satisfactory to the
Administrator for payment of any Federal, state, and local taxes required by law
to be withheld on account of such taxable event. Except in the case where an
election is made pursuant to Paragraph 8 below, the Grantee may elect to have
the required minimum tax withholding obligation satisfied, in whole or in part,
by authorizing the Company to withhold from shares of Stock to be issued or
released by the transfer agent a number of shares of Stock with an aggregate
Fair Market Value that would satisfy the withholding amount due.

        8.    Election Under Section 83(b).    The Grantee and the Company
hereby agree that the Grantee may, within 30 days following the acceptance of
this Award as provided in Paragraph 1 hereof, file with the Internal Revenue
Service and the Company an election under Section 83(b) of the Internal Revenue
Code. In the event the Grantee makes such an election, he or she agrees to
provide a copy of the election to the Company.

        9.    No Obligation to Continue Employment.    Neither the Company nor
any Subsidiary is obligated by or as a result of the Plan or this Agreement to
continue the Grantee in employment and neither the Plan nor this Agreement shall
interfere in any way with the right of the Company or any Subsidiary to
terminate the employment of the Grantee at any time.

        10.    Notices.    Notices hereunder shall be mailed or delivered to the
Company at its principal place of business and shall be mailed or delivered to
the Grantee at the address on file with the Company or, in either case, at such
other address as one party may subsequently furnish to the other party in
writing.

        HELICOS BIOSCIENCES CORPORATION
 
 
 
 
By:
 
             

--------------------------------------------------------------------------------

Title:

2

--------------------------------------------------------------------------------

        The foregoing Agreement is hereby accepted and the terms and conditions
thereof hereby agreed to by the undersigned.

Dated:                

--------------------------------------------------------------------------------

   

--------------------------------------------------------------------------------

Optionee's Signature
 
 
 
 
Optionee's name and address:
 
 
 
 

--------------------------------------------------------------------------------

         

--------------------------------------------------------------------------------

         

--------------------------------------------------------------------------------

3

--------------------------------------------------------------------------------

NON-QUALIFIED STOCK OPTION AGREEMENT
FOR NON-EMPLOYEE DIRECTORS
UNDER THE HELICOS BIOSCIENCES CORPORATION
2007 STOCK OPTION AND INCENTIVE PLAN

Name of Optionee:  

--------------------------------------------------------------------------------

      No. of Option Shares:  

--------------------------------------------------------------------------------

      Option Exercise Price per Share: $  

--------------------------------------------------------------------------------

     
[FMV on Grant Date]
 
 
Grant Date:
 

--------------------------------------------------------------------------------

 
 
  Vesting Start Date:  

--------------------------------------------------------------------------------

      Expiration Date: Ten Years from Grant Date    

        Pursuant to the Helicos Biosciences Corporation 2007 Stock Option and
Incentive Plan as amended through the date hereof (the "Plan"), Helicos
Biosciences Corporation (the "Company") hereby grants to the Optionee named
above, who is a Director of the Company but is not an employee of the Company,
an option (the "Stock Option") to purchase on or prior to the Expiration Date
specified above all or part of the number of shares of Common Stock, par value
$0.001 per share (the "Stock"), of the Company specified above at the Option
Exercise Price per Share specified above subject to the terms and conditions set
forth herein and in the Plan. This Stock Option is not intended to be an
"incentive stock option" under Section 422 of the Internal Revenue Code of 1986,
as amended.

        1.    Exercisability Schedule.    No portion of this Stock Option may be
exercised until such portion shall have become exercisable. Except as set forth
below, and subject to the discretion of the Administrator (as defined in
Section 2 of the Plan) to accelerate the exercisability schedule hereunder, this
Stock Option shall be exercisable with respect to the following number of Option
Shares on the dates indicated:

Incremental Number of
Option Shares Exercisable
  Exercisability Date 100% of Shares   One year from Vesting Start Date

        In the event of the termination of the Optionee's service as a director
of the Company because of death, this Stock Option shall become immediately
exercisable in full, whether or not exercisable at such time. Once exercisable,
this Stock Option shall continue to be exercisable at any time or times prior to
the close of business on the Expiration Date, subject to the provisions hereof
and of the Plan.

        2.    Manner of Exercise.    

        (a)    The Optionee may exercise this Stock Option only in the following
manner: from time to time on or prior to the Expiration Date of this Stock
Option, the Optionee may give written notice to the Administrator of his or her
election to purchase some or all of the Option Shares purchasable at the time of
such notice. This notice shall specify the number of Option Shares to be
purchased.

        Payment of the purchase price for the Option Shares may be made by one
or more of the following methods: (i) in cash, by certified or bank check or
other instrument acceptable to the Administrator; (ii) through the delivery (or
attestation to the ownership) of shares of Stock that have been purchased by the
Optionee on the open market or that are beneficially owned by the Optionee and
are not then subject to any restrictions under any Company plan and that
otherwise satisfy any holding periods as may be required by the Administrator;
(iii) by the Optionee delivering to the Company a properly executed exercise
notice together with irrevocable instructions to a broker to promptly deliver to
the Company cash or a check payable and acceptable to the Company to pay the
option purchase price, provided that in the event the Optionee chooses to pay
the option purchase price as so provided, the Optionee and the broker shall
comply with such procedures and enter into

--------------------------------------------------------------------------------

such agreements of indemnity and other agreements as the Administrator shall
prescribe as a condition of such payment procedure; or (iv) a combination of
(i), (ii) and (iii) above. Payment instruments will be received subject to
collection.

        The transfer to the Optionee on the records of the Company or of the
transfer agent of the Option Shares will be contingent upon (i) the Company's
receipt from the Optionee of the full purchase price for the Option Shares, as
set forth above, (ii) the fulfillment of any other requirements contained herein
or in the Plan or in any other agreement or provision of laws, and (iii) the
receipt by the Company of any agreement, statement or other evidence that the
Company may require to satisfy itself that the issuance of Stock to be purchased
pursuant to the exercise of Stock Options under the Plan and any subsequent
resale of the shares of Stock will be in compliance with applicable laws and
regulations. In the event the Optionee chooses to pay the purchase price by
previously-owned shares of Stock through the attestation method, the number of
shares of Stock transferred to the Optionee upon the exercise of the Stock
Option shall be net of the Shares attested to.

        (b)    The shares of Stock purchased upon exercise of this Stock Option
shall be transferred to the Optionee on the records of the Company or of the
transfer agent upon compliance to the satisfaction of the Administrator with all
requirements under applicable laws or regulations in connection with such
transfer and with the requirements hereof and of the Plan. The determination of
the Administrator as to such compliance shall be final and binding on the
Optionee. The Optionee shall not be deemed to be the holder of, or to have any
of the rights of a holder with respect to, any shares of Stock subject to this
Stock Option unless and until this Stock Option shall have been exercised
pursuant to the terms hereof, the Company or the transfer agent shall have
transferred the shares to the Optionee, and the Optionee's name shall have been
entered as the stockholder of record on the books of the Company. Thereupon, the
Optionee shall have full voting, dividend and other ownership rights with
respect to such shares of Stock.

        (c)    The minimum number of shares with respect to which this Stock
Option may be exercised at any one time shall be 100 shares, unless the number
of shares with respect to which this Stock Option is being exercised is the
total number of shares subject to exercise under this Stock Option at the time.

        (d)    Notwithstanding any other provision hereof or of the Plan, no
portion of this Stock Option shall be exercisable after the Expiration Date
hereof.

        3.    Termination as Director.    If the Optionee ceases to be a
Director of the Company, the period within which to exercise the Stock Option
may be subject to earlier termination as set forth below.

        (a)    Termination by Reason of Death.    If the Optionee ceases to be a
Director by reason of the Optionee's death, any portion of this Stock Option
outstanding on such date may be exercised by his or her legal representative or
legatee for a period of 12 months from the date of death or until the Expiration
Date, if earlier.

        (b)    Other Termination.    If the Optionee ceases to be a Director for
any reason other than the Optionee's death, any portion of this Stock Option
outstanding on such date may be exercised for a period of 12 months from the
date of termination or until the Expiration Date, if earlier.

        4.    Incorporation of Plan.    Notwithstanding anything herein to the
contrary, this Stock Option shall be subject to and governed by all the terms
and conditions of the Plan, including the powers of the Administrator set forth
in Section 2(b) of the Plan. Capitalized terms in this Agreement shall have the
meaning specified in the Plan, unless a different meaning is specified herein.

        5.    Transferability.    This Agreement is personal to the Optionee, is
non-assignable and is not transferable in any manner, by operation of law or
otherwise, other than by will or the laws of descent and distribution. This
Stock Option is exercisable, during the Optionee's lifetime, only by the
Optionee, and thereafter, only by the Optionee's legal representative or
legatee.

2

--------------------------------------------------------------------------------

        6.    No Obligation to Continue as a Director.    Neither the Plan nor
this Stock Option confers upon the Optionee any rights with respect to
continuance as a Director.

        7.    Notices.    Notices hereunder shall be mailed or delivered to the
Company at its principal place of business and shall be mailed or delivered to
the Optionee at the address on file with the Company or, in either case, at such
other address as one party may subsequently furnish to the other party in
writing.

        8.    Amendment.    Pursuant to Section 16 of the Plan, the
Administrator may at any time amend or cancel any outstanding portion of this
Stock Option, but no such action may be taken that adversely affects the
Optionee's rights under this Agreement without the Optionee's consent.

        HELICOS BIOSCIENCES CORPORATION
 
 
 
 
By:
 
             

--------------------------------------------------------------------------------

Title:

        The foregoing Agreement is hereby accepted and the terms and conditions
thereof hereby agreed to by the undersigned.

Dated:                

--------------------------------------------------------------------------------

   

--------------------------------------------------------------------------------

Optionee's Signature
 
 
 
 
Optionee's name and address:
 
 
 
 

--------------------------------------------------------------------------------

         

--------------------------------------------------------------------------------

         

--------------------------------------------------------------------------------

3

--------------------------------------------------------------------------------

QuickLinks

EXHIBIT 10.1