<PAGE>
                                                                   Exhibit 10.29

                          IDENIX PHARMACEUTICALS, INC.

                       Nonstatutory Stock Option Agreement
                     Granted Under 2004 Stock Incentive Plan

1.   Grant of Option.

     This agreement evidences the grant by Idenix Pharmaceuticals, Inc., a
[Delaware] corporation (the "Company"), on ____________, 200[ ] (the "Grant
Date") to [____________] (the "Participant"), of an option to purchase (the
"Option"), in whole or in part, on the terms provided herein and in the
Company's 2004 Stock Incentive Plan (the "Plan"), a total of [________] shares
(the "Shares") of common stock, $.001 par value per share, of the Company
("Common Stock") at $[____________] per Share. Unless earlier terminated, this
Option shall expire at 5:00 p.m., Eastern time, on [____________] (the "Final
Exercise Date").

     It is intended that the Option evidenced by this agreement shall not be an
incentive stock option as defined in Section 422 of the Internal Revenue Code of
1986, as amended, and any regulations promulgated thereunder (the "Code").
Except as otherwise indicated by the context, the term "Participant", as used in
this Option, shall be deemed to include any person who acquires the right to
exercise this Option validly under its terms.

2.   Vesting Schedule.

     This Option will become exercisable ("vest") ratably over a 48 month
beginning on the last day of the month in which the grant occurs and continuing
thereafter on the last day of each of the next 47 successive months.

     The right of exercise shall be cumulative so that to the extent the Option
is not exercised in any period to the maximum extent permissible it shall
continue to be exercisable, in whole or in part, with respect to all Shares for
which it is vested until the earlier of the Final Exercise Date or the
termination of this Option under Section 3 hereof or the Plan.

3.   Exercise of Option.

     (a) Form of Exercise. Each election to exercise this Option shall be in
writing, signed by the Participant, and received by the Company at its principal
office, accompanied by this agreement, and payment in full in the manner
provided in the Plan. The Participant may purchase less than the number of
shares covered hereby, provided that no partial exercise of this Option may be
for any fractional share or for fewer than ten whole shares.

     (b) Continuous Relationship with the Company Required. Except as otherwise
provided in this Section 3, this Option may not be exercised unless the
Participant, at the time he or she exercises this Option, is, and has been at
all times since the Grant Date, an employee or officer of, or consultant or
advisor to, the Company or any other entity the employees, officers, directors,
consultants, or advisors of which are eligible to receive option grants under
the Plan (an "Eligible Participant").

     (c) Termination of Relationship with the Company. If the Participant ceases
to be an Eligible Participant for any reason, then, except as provided in
paragraphs (d) and (e) below, the right to exercise this Option shall terminate
180 days after such cessation (but in no event after the Final Exercise Date),
provided that this Option shall be exercisable only to the extent that the
Participant was entitled to exercise this Option on the date of such cessation.
Notwithstanding the foregoing, if the Participant, prior

<PAGE>

to the Final Exercise Date, violates the non-competition or confidentiality
provisions of any employment contract, confidentiality and nondisclosure
agreement or other agreement between the Participant and the Company, the right
to exercise this Option shall terminate immediately upon such violation.

     (d) Exercise Period Upon Death or Disability. If the Participant dies or
becomes disabled (within the meaning of Section 22(e)(3) of the Code) prior to
the Final Exercise Date while he or she is an Eligible Participant and the
Company has not terminated such relationship for "cause" as specified in
paragraph (e) below, this Option shall be exercisable, within the period of one
year following the date of death or disability of the Participant, by the
Participant (or in the case of death by an authorized transferee), provided that
this Option shall be exercisable only to the extent that this Option was
exercisable by the Participant on the date of his or her death or disability,
and further provided that this Option shall not be exercisable after the Final
Exercise Date.

     (e) Discharge for Cause. If the Participant, prior to the Final Exercise
Date, is discharged by the Company for "cause" (as defined below), the right to
exercise this Option shall terminate immediately upon the effective date of such
discharge. "Cause" shall mean willful misconduct by the Participant or willful
failure by the Participant to perform his or her responsibilities to the Company
(including, without limitation, breach by the Participant of any provision of
any employment, consulting, advisory, nondisclosure, non-competition or other
similar agreement between the Participant and the Company), as determined by the
Company, which determination shall be conclusive. The Participant shall be
considered to have been discharged for "Cause" if the Company determines, within
30 days after the Participant's resignation, that discharge for cause was
warranted.

4.   Agreement in Connection with Public Offering.

     The Participant agrees, in connection with an underwritten public offering
of the Company's securities pursuant to a registration statement under the
Securities Act, (i) not to sell, make short sale of, loan, grant any options for
the purchase of, or otherwise dispose of any shares of Common Stock held by the
Participant (other than those shares included in the offering) without the prior
written consent of the Company or the underwriters managing such underwritten
public offering of the Company's securities for a period of 180 days from the
effective date of such registration statement, and (ii) to execute any agreement
reflecting clause (i) above as may be requested by the Company or the managing
underwriters at the time of such offering.

5.   Withholding.

     No Shares will be issued pursuant to the exercise of this Option unless and
until the Participant pays to the Company, or makes provision satisfactory to
the Company for payment of, any federal, state or local withholding taxes
required by law to be withheld in respect of this Option.

6.   Nontransferability of Option.

     This Option may not be sold, assigned, transferred, pledged or otherwise
encumbered by the Participant, either voluntarily or by operation of law, except
by will or the laws of descent and distribution, and, during the lifetime of the
Participant, this Option shall be exercisable only by the Participant.

7.   Provisions of the Plan.

     This Option is subject to the provisions of the Plan, a copy of which is
furnished to the Participant with this Option.


                                      -2-

<PAGE>

     IN WITNESS WHEREOF, the Company has caused this agreement to be executed
under its corporate seal by its duly authorized officer. This agreement shall
take effect as a sealed instrument.

                                        IDENIX PHARMACEUTICALS, INC.


Dated:                                  By:
       -------------                        ------------------------------------
                                        Name:
                                              ----------------------------------
                                        Title:
                                               ---------------------------------


                                      -3-

<PAGE>

                            PARTICIPANT'S ACCEPTANCE

     The undersigned hereby accepts the foregoing Option and agrees to the terms
and conditions thereof. The undersigned hereby acknowledges receipt of a copy of
the Company's 2004 Stock Incentive Plan.

                                        PARTICIPANT:

                                        ----------------------------------------
                                        Address:
                                                 -------------------------------

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


                                      -4-