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Exhibit 10.1

OPTIMER PHARMACEUTICALS, INC.
EMPLOYEE STOCK PURCHASE PLAN

        1.    Purpose.    The purpose of the Plan is to provide employees of the
Company and its Designated Subsidiaries with an opportunity to purchase Common
Stock of the Company through accumulated payroll deductions. It is the intention
of the Company to have the Plan qualify as an "Employee Stock Purchase Plan"
under Section 423 of the Code. The provisions of the Plan, accordingly, shall be
construed so as to extend and limit participation in a uniform and
nondiscriminatory basis consistent with the requirements of Section 423.

        2.    Definitions.    

        (a)   "Administrator" shall mean the Board or any Committee designated
by the Board to administer the plan pursuant to Section 14.

        (b)   "Board" shall mean the Board of Directors of the Company.

        (c)   "Change in Control" means the occurrence of any of the following
events:

          (i)  Any "person" (as such term is used in Sections 13(d) and 14(d) of
the Exchange Act) becomes the "beneficial owner" (as defined in Rule 13d-3 of
the Exchange Act), directly or indirectly, of securities of the Company
representing fifty percent (50%) or more of the total voting power represented
by the Company's then outstanding voting securities; or

         (ii)  The consummation of the sale or disposition by the Company of all
or substantially all of the Company's assets; or

        (iii)  A change in the composition of the Board occurring within a
two-year period, as a result of which fewer than a majority of the directors are
Incumbent Directors. "Incumbent Directors" means directors who either (A) are
Directors as of the effective date of the Plan, or (B) are elected, or nominated
for election, to the Board with the affirmative votes of at least a majority of
the Directors at the time of such election or nomination (but will not include
an individual whose election or nomination is in connection with an actual or
threatened proxy contest relating to the election of directors to the
Company); or

        (iv)  The consummation of a merger or consolidation of the Company with
any other corporation, other than a merger or consolidation which would result
in the voting securities of the Company outstanding immediately prior thereto
continuing to represent (either by remaining outstanding or by being converted
into voting securities of the surviving entity or its parent) at least fifty
percent (50%) of the total voting power represented by the voting securities of
the Company or such surviving entity or its parent outstanding immediately after
such merger or consolidation.

        (d)   "Code" shall mean the Internal Revenue Code of 1986, as amended.

        (e)   "Committee" means a committee of the Board appointed in accordance
with Section 14 hereof.

        (f)    "Common Stock" shall mean the common stock of the Company.

        (g)   "Company" shall mean Optimer Pharmaceuticals, Inc., a Delaware
corporation.

        (h)   "Compensation" shall mean all base straight time gross earnings,
commissions, overtime and shift premium, but exclusive of payments for incentive
compensation, bonuses and other compensation.

        (i)    "Designated Subsidiary" shall mean any Subsidiary selected by the
Administrator as eligible to participate in the Plan.

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        (j)    "Director" shall mean a member of the Board.

        (k)   "Eligible Employee" shall mean any individual who is a common law
employee of the Company or any Designated Subsidiary and whose customary
employment with the Company or Designated Subsidiary is at least twenty
(20) hours per week and more than five (5) months in any calendar year. For
purposes of the Plan, the employment relationship shall be treated as continuing
intact while the individual is on sick leave or other leave of absence approved
by the Company. Where the period of leave exceeds 90 days and the individual's
right to reemployment is not guaranteed either by statute or by contract, the
employment relationship shall be deemed to have terminated on the 91st day of
such leave.

        (l)    "Exchange Act" shall mean the Securities Exchange Act of 1934, as
amended.

        (m)  "Exercise Date" shall mean the first Trading Day on or after May 15
and November 15 of each year. The first Exercise Date under the Plan shall be
November 15, 2007.

        (n)   "Fair Market Value" shall mean, as of any date and unless the
Administrator determines otherwise, the value of Common Stock determined
as follows:

          (i)  If the Common Stock is listed on any established stock exchange
or a national market system, including without limitation the Nasdaq Global
Market, its Fair Market Value shall be the closing sales price for such stock
(or the closing bid, if no sales were reported) as quoted on such exchange or
system on the date of determination, as reported in The Wall Street Journal or
such other source as the Board deems reliable;

         (ii)  If the Common Stock is regularly quoted by a recognized
securities dealer but selling prices are not reported, its Fair Market Value
shall be the mean of the closing bid and asked prices for the Common Stock on
the date of determination, as reported in The Wall Street Journal or such other
source as the Board deems reliable;

        (iii)  In the absence of an established market for the Common Stock, the
Fair Market Value thereof shall be determined in good faith by the Board; or

        (iv)  For purposes of the Offering Date of the first Offering Period
under the Plan, the Fair Market Value shall be the initial price to the public
as set forth in the final prospectus included within the registration statement
on Form S-1 filed with the Securities and Exchange Commission for the initial
public offering of the Company's Common Stock (the "Registration Statement").

        (o)   "Fiscal Year" means the fiscal year of the Company.

        (p)   "Offering Date" shall mean the first Trading Day of each Offering
Period.

        (q)   "Offering Periods" shall mean the periods of approximately six
(6) months during which an option granted pursuant to the Plan may be exercised,
commencing on the first Trading Day on or after May 15 and November 15 of each
year and terminating on the first Trading Day on or after the subsequent
Offering Period commencement date approximately six months later; provided,
however, that the first Offering Period under the Plan shall commence with the
first Trading Day on or after the date on which the Securities and Exchange
Commission declares the Company's registration statement on Form S-1 effective
and end on the first Trading Day on or after November 15, 2007 and the second
Offering Period under the Plan shall commence with the first Trading Day on or
after November 16, 2007. The duration and timing of Offering Periods may be
changed pursuant to Section 4 of this Plan.

        (r)   "Plan" shall mean this Optimer Pharmaceuticals, Inc. Employee
Stock Purchase Plan.

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        (s)   "Purchase Price" shall mean an amount equal to eighty-five percent
(85%) of the Fair Market Value of a share of Common Stock on the Offering Date
or on the Exercise Date, whichever is lower; provided however, that the Purchase
Price may be determined for subsequent Offering Periods by the Administrator
subject to compliance with Section 423 of the Code (or any successor rule or
provision or any other applicable law, regulation or stock exchange rule) or
pursuant to Section 20.

        (t)    "Subsidiary" shall mean a "subsidiary corporation," whether now
or hereafter existing, as defined in Section 424(f) of the Code.

        (u)   "Trading Day" shall mean a day on which the national stock
exchange upon which the Company Common Stock is listed is open for trading.

        3.    Eligibility.    

        (a)   First Offering Period.    Any individual who is an Eligible
Employee immediately prior to the first Offering Period shall be automatically
enrolled in the first Offering Period.

        (b)   Subsequent Offering Periods.    Any Eligible Employee on a given
Offering Date shall be eligible to participate in the Plan.

        (c)   Limitations.    Any provisions of the Plan to the contrary
notwithstanding, no Eligible Employee shall be granted an option under the Plan
(i) to the extent that, immediately after the grant, such Eligible Employee
(or any other person whose stock would be attributed to such Eligible Employee
pursuant to Section 424(d) of the Code) would own capital stock of the Company
and/or hold outstanding options to purchase such stock possessing five percent
(5%) or more of the total combined voting power or value of all classes of the
capital stock of the Company or of any Subsidiary, or (ii) to the extent that
his or her rights to purchase stock under all employee stock purchase plans of
the Company and its subsidiaries accrues at a rate which exceeds Twenty-Five
Thousand Dollars ($25,000) worth of stock (determined at the fair market value
of the shares at the time such option is granted) for each calendar year in
which such option is outstanding at any time.

        4.    Offering Periods.    The Plan shall be implemented by consecutive
Offering Periods with a new Offering Period commencing on the first Trading Day
on or after May 15 and November 15 each year, or on such other date as the Board
shall determine; provided, however, that the first Offering Period under the
Plan shall commence with the first Trading Day on or after the date upon which
the Company's Registration Statement is declared effective by the Securities and
Exchange Commission and end on the first Trading Day on or after November 15,
2007. The Board shall have the power to change the duration of Offering Periods
(including the commencement dates thereof) with respect to future offerings
without stockholder approval if such change is announced prior to the scheduled
beginning of the first Offering Period to be affected thereafter.

        5.    Participation.    

        (a)   First Offering Period.    An Eligible Employee shall be entitled
to participate in the first Offering Period only if such individual submits a
subscription agreement authorizing payroll deductions in a form determined by
the Administrator (which may be similar to the form attached hereto as
Exhibit A) to the Company's designated plan administrator (i) no earlier than
the effective date of the Form S-8 registration statement with respect to the
issuance of Common Stock under this Plan and (ii) no later than twenty
(20) business days following the effective date of such S-8 registration
statement (the "Enrollment Window"). An Eligible Employee's failure to submit
the subscription agreement during the Enrollment Window shall result in the
automatic termination of such individual's participation in the Offering Period.

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        (b)   Subsequent Offering Periods.    An Eligible Employee may become a
participant in the Plan by completing a subscription agreement in a form
determined by the Administrator (which may be similar to the form attached
hereto as Exhibit A) and filing it with the Company's designated Plan
administrator prior to the applicable Offering Date.

        6.    Payroll Deductions.    

        (a)   At the time a participant files his or her subscription agreement,
he or she shall elect to have payroll deductions made on each pay day during the
Offering Period in an amount not exceeding 10% of the Compensation which he or
she receives on each pay day during the Offering Period; provided, however, that
should a pay day occur on an Exercise Date, a participant shall have the payroll
deductions made on such day applied to his or her account under the new Offering
Period. A participant's subscription agreement shall remain in effect for
successive Offering Periods unless terminated as provided in Section 10 hereof.

        (b)   Payroll deductions for a participant shall commence on the first
pay day following the Offering Date and shall end on the last pay day in the
Offering Period to which such authorization is applicable, unless sooner
terminated by the participant as provided in Section 10 hereof; provided,
however, that for the first Offering Period, payroll deductions shall commence
on the first pay day on or following the end of the Enrollment Window.

        (c)   All payroll deductions made for a participant shall be credited to
his or her account under the Plan and shall be withheld in whole percentages
only. A participant may not make any additional payments into such account.

        (d)   A participant may discontinue his or her participation in the Plan
as provided in Section 10 hereof, or may increase or decrease the rate of his or
her payroll deductions during the Offering Period by completing or filing with
the Company a new subscription agreement authorizing a change in payroll
deduction rate. The Administrator may, in its discretion, limit the nature
and/or number of participation rate changes during any Offering Period. The
change in rate shall be effective with the first full payroll period following
five (5) business days after the Company's receipt of the new subscription
agreement unless the Company elects to process a given change in participation
more quickly.

        (e)   Notwithstanding the foregoing, to the extent necessary to comply
with Section 423(b)(8) of the Code and Section 3(c) hereof, a participant's
payroll deductions may be decreased to zero percent (0%) at any time during an
Offering Period. Payroll deductions shall recommence at the rate provided in
such participant's subscription agreement at the beginning of the first Offering
Period which is scheduled to end in the following calendar year, unless
terminated by the participant as provided in Section 10 hereof.

        (f)    At the time the option is exercised, in whole or in part, or at
the time some or all of the Company's Common Stock issued under the Plan is
disposed of, the participant must make adequate provision for the Company's or
its Subsidiary's federal, state, or any other tax liability payable to any
authority, national insurance, social security or other tax withholding
obligations, if any, which arise upon the exercise of the option or the
disposition of the Common Stock. At any time, the Company or its Subsidiary may,
but shall not be obligated to, withhold from the participant's compensation the
amount necessary for the Company or its Subsidiary to meet applicable
withholding obligations, including any withholding required to make available to
the Company or its Subsidiary any tax deductions or benefits attributable to
sale or early disposition of Common Stock by the Eligible Employee.

        7.    Grant of Option.    On the Offering Date of each Offering Period,
each Eligible Employee participating in such Offering Period shall be granted an
option to purchase on each Exercise Date during such Offering Period (at the
applicable Purchase Price) up to a number of shares of the

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Company's Common Stock determined by dividing such Eligible Employee's payroll
deductions accumulated prior to such Exercise Date by the applicable Purchase
Price; provided that in no event shall an Eligible Employee be permitted to
purchase during the first Offering Period more than 1,000 shares of the
Company's Common Stock and no more than 2,500 shares of the Company's Common
Stock during any subsequent Offering Period (subject to any adjustment pursuant
to Section 19), and provided further that such purchase shall be subject to the
limitations set forth in Sections 3(c) and 13 hereof. The Eligible Employee may
accept the grant of such option by turning in a completed Subscription Agreement
(attached hereto as Exhibit A) to the Company on or prior to an Offering Date,
or with respect to the first Offering Period, prior to the last day of the
Enrollment Window. The Administrator may, for future Offering Periods, increase
or decrease, in its absolute discretion, the maximum number of shares of the
Company's Common Stock an Eligible Employee may purchase during each Offering
Period. Exercise of the option shall occur as provided in Section 8 hereof,
unless the participant has withdrawn pursuant to Section 10 hereof. The option
shall expire on the last day of the Offering Period.

        8.    Exercise of Option.    

        (a)   Unless a participant withdraws from the Plan as provided in
Section 10 hereof, his or her option for the purchase of shares shall be
exercised automatically on the Exercise Date, and the maximum number of full
shares subject to option shall be purchased for such participant at the
applicable Purchase Price with the accumulated payroll deductions in his or her
account. No fractional shares shall be purchased; any payroll deductions
accumulated in a participant's account which are not sufficient to purchase a
full share shall be retained in the participant's account for the subsequent
Offering Period, subject to earlier withdrawal by the participant as provided in
Section 10 hereof. Any other funds left over in a participant's account after
the Exercise Date shall be returned to the participant. During a participant's
lifetime, a participant's option to purchase shares hereunder is exercisable
only by him or her.

        (b)   If the Administrator determines that, on a given Exercise Date,
the number of shares with respect to which options are to be exercised may
exceed (i) the number of shares of Common Stock that were available for sale
under the Plan on the Offering Date of the applicable Offering Period, or
(ii) the number of shares available for sale under the Plan on such Exercise
Date, the Administrator may in its sole discretion provide that the Company
shall make a pro rata allocation of the shares of Common Stock available for
purchase on such Exercise Date in as uniform a manner as shall be practicable
and as it shall determine in its sole discretion to be equitable among all
participants exercising options to purchase Common Stock on such Exercise Date.
The Company may make a pro rata allocation of the shares available on the
Offering Date of any applicable Offering Period pursuant to the preceding
sentence, notwithstanding any authorization of additional shares for issuance
under the Plan by the Company's stockholders subsequent to such Offering Date.

        9.    Delivery.    As soon as reasonably practicable after each Exercise
Date on which a purchase of shares occurs, the Company shall arrange the
delivery to each participant the shares purchased upon exercise of his or her
option in a form determined by the Administrator.

        10.    Withdrawal.    

        (a)   A participant may withdraw all but not less than all the payroll
deductions credited to his or her account and not yet used to exercise his or
her option under the Plan at any time by giving written notice to the Company in
the form determined by the Administrator (which may be similar to the form
attached as Exhibit B to this Plan). All of the participant's payroll deductions
credited to his or her account shall be paid to such participant promptly after
receipt of notice of withdrawal and such participant's option for the Offering
Period shall be automatically terminated, and no further payroll deductions for
the purchase of shares shall be made for such Offering Period. If a participant
withdraws from an Offering Period, payroll deductions shall not resume at

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the beginning of the succeeding Offering Period unless the participant delivers
to the Company a new subscription agreement.

        (b)   A participant's withdrawal from an Offering Period shall not have
any effect upon his or her eligibility to participate in any similar plan which
may hereafter be adopted by the Company or in succeeding Offering Periods which
commence after the termination of the Offering Period from which the participant
withdraws.

        11.    Termination of Employment.    Upon a participant's ceasing to be
an Eligible Employee, for any reason, he or she shall be deemed to have elected
to withdraw from the Plan and the payroll deductions credited to such
participant's account during the Offering Period but not yet used to purchase
shares of Common Stock under the Plan shall be returned to such participant or,
in the case of his or her death, to the person or persons entitled thereto under
Section 15, and such participant's option shall be automatically terminated.

        12.    Interest.    No interest shall accrue on the payroll deductions
of a participant in the Plan.

        13.    Stock.    

        (a)   Subject to adjustment upon changes in capitalization of the
Company as provided in Section 19 hereof, the maximum number of shares of the
Company's Common Stock which shall be made available for sale under the Plan
shall be 200,000 shares (which has been determined after adjustment to reflect
the stock split which will be completed by the Company prior to the initial
registration of the Company's Common Stock under Section 12 of the Exchange Act)
plus an annual increase to be added on the first day of each Company Fiscal Year
beginning with the 2008 Fiscal Year, equal to the lesser of (i) 300,000 shares
of Common Stock (which has been determined after adjustment to reflect the stock
split which will be completed by the Company prior to the initial registration
of the Company's Common Stock under Section 12 of the Exchange Act), (ii) three
percent (3%) of the outstanding shares of Common Stock on the last day of the
immediately preceding Fiscal Year or (iii) an amount determined by the Board.

        (b)   Until the shares are issued (as evidenced by the appropriate entry
on the books of the Company or of a duly authorized transfer agent of the
Company), a participant shall only have the rights of an unsecured creditor with
respect to such shares, and no right to vote or receive dividends or any other
rights as a stockholder shall exist with respect to such shares.

        (c)   Shares to be delivered to a participant under the Plan shall be
registered in the name of the participant or in the name of the participant and
his or her spouse.

        14.    Administration.    The Plan will be administered by an
Administrator which shall be either (A) the Board or (B) a Committee appointed
by the Board, which committee will be constituted to satisfy all applicable law.
The Administrator shall administer the Plan and shall have full and exclusive
discretionary authority to construe, interpret and apply the terms of the Plan,
to determine eligibility and to adjudicate all disputed claims filed under the
Plan. Every finding, decision and determination made by the Administrator shall,
to the full extent permitted by law, be final and binding upon all parties.
Notwithstanding any provision to the contrary in this Plan, the Administrator
may adopt rules or procedures relating to the operation and administration of
the Plan to accommodate the specific requirements of local laws and procedures
for jurisdictions outside of the United States. Without limiting the generality
of the foregoing, the Administrator is specifically authorized to adopt rules
and procedures regarding eligibility to participate, the definition of
Compensation, handling of payroll deductions, making of contributions to the
Plan (including, without limitation, in forms other than payroll deductions),
establishment of bank or trust accounts to hold payroll deductions, payment of
interest, conversion of local currency, obligations to pay payroll tax,
determination of beneficiary designation requirements, withholding procedures
and handling of stock certificates which vary with local requirements.

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        15.    Designation of Beneficiary.    

        (a)   A participant may file a designation of a beneficiary who is to
receive any shares and cash, if any, from the participant's account under the
Plan in the event of such participant's death subsequent to an Exercise Date on
which the option is exercised but prior to delivery to such participant of such
shares and cash. In addition, a participant may file a designation of a
beneficiary who is to receive any cash from the participant's account under the
Plan in the event of such participant's death prior to exercise of the option.
If a participant is married and the designated beneficiary is not the spouse,
spousal consent shall be required for such designation to be effective.

        (b)   Such designation of beneficiary may be changed by the participant
at any time by notice in a form determined by the Administrator. In the event of
the death of a participant and in the absence of a beneficiary validly
designated under the Plan who is living at the time of such participant's death,
the Company shall deliver such shares and/or cash to the executor or
administrator of the estate of the participant, or if no such executor or
administrator has been appointed (to the knowledge of the Company), the Company,
in its discretion, may deliver such shares and/or cash to the spouse or to any
one or more dependents or relatives of the participant, or if no spouse,
dependent or relative is known to the Company, then to such other person as the
Company may designate.

        (c)   All beneficiary designations shall be in such form and manner as
the Administrator may designate from time to time.

        16.    Transferability.    Neither payroll deductions credited to a
participant's account nor any rights with regard to the exercise of an option or
to receive shares under the Plan may be assigned, transferred, pledged or
otherwise disposed of in any way (other than by will, the laws of descent and
distribution or as provided in Section 15 hereof) by the participant. Any such
attempt at assignment, transfer, pledge or other disposition shall be without
effect, except that the Company may treat such act as an election to withdraw
funds from an Offering Period in accordance with Section 10 hereof.

        17.    Use of Funds.    All payroll deductions received or held by the
Company under the Plan may be used by the Company for any corporate purpose, and
the Company shall not be obligated to segregate such payroll deductions. Until
shares are issued, participants shall only have the rights of an unsecured
creditor.

        18.    Reports.    Individual accounts shall be maintained for each
participant in the Plan. Statements of account shall be given to participating
Eligible Employees at least annually, which statements shall set forth the
amounts of payroll deductions, the Purchase Price, the number of shares
purchased and the remaining cash balance, if any.

        19.    Adjustments Upon Changes in Capitalization, Dissolution,
Liquidation, Merger or Change in Control.    

        (a)   Changes in Capitalization.    Subject to any required action by
the stockholders of the Company, the maximum number of shares of the Company's
Common Stock which shall be made available for sale under the Plan, the maximum
number of shares each participant may purchase each Offering Period (pursuant to
Section 7), as well as the price per share and the number of shares of Common
Stock covered by each option under the Plan which has not yet been exercised
shall be proportionately adjusted for any increase or decrease in the number of
issued shares of Common Stock resulting from a stock split, reverse stock split,
stock dividend, combination or reclassification of the Common Stock, or any
other change in the number of shares of Common Stock effected without receipt of
consideration by the Company; provided, however, that conversion of any
convertible securities of the Company shall not be deemed to have been "effected
without receipt of consideration." Such adjustment shall be made by the
Administrator,

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whose determination in that respect shall be final, binding and conclusive.
Except as expressly provided herein, no issuance by the Company of shares of
stock of any class, or securities convertible into shares of stock of any class,
shall affect, and no adjustment by reason thereof shall be made with respect to,
the number or price of shares of Common Stock subject to an option.

        (b)   Dissolution or Liquidation.    In the event of the proposed
dissolution or liquidation of the Company, the Offering Period then in progress
shall be shortened by setting a new Exercise Date (the "New Exercise Date"), and
shall terminate immediately prior to the consummation of such proposed
dissolution or liquidation, unless provided otherwise by the Administrator. The
New Exercise Date shall be before the date of the Company's proposed dissolution
or liquidation. The Administrator shall notify each participant in writing, at
least ten (10) business days prior to the New Exercise Date, that the Exercise
Date for the participant's option has been changed to the New Exercise Date and
that the participant's option shall be exercised automatically on the
New Exercise Date, unless prior to such date the participant has withdrawn from
the Offering Period as provided in Section 10 hereof.

        (c)   Merger or Change in Control.    In the event of a merger or Change
in Control, each outstanding option shall be assumed or an equivalent option
substituted by the successor corporation or a Parent or Subsidiary of the
successor corporation. In the event that the successor corporation refuses to
assume or substitute for the option, the Offering Period then in progress shall
be shortened by setting a New Exercise Date and shall end on the New Exercise
Date. The New Exercise Date shall be before the date of the Company's proposed
merger or Change in Control. The Administrator shall notify each participant in
writing, at least ten (10) business days prior to the New Exercise Date, that
the Exercise Date for the participant's option has been changed to the
New Exercise Date and that the participant's option shall be exercised
automatically on the New Exercise Date, unless prior to such date the
participant has withdrawn from the Offering Period as provided in
Section 10 hereof.

        20.    Amendment or Termination.    

        (a)   The Administrator may at any time and for any reason terminate or
amend the Plan. Except as provided in Section 19 and this Section 20 hereof, no
amendment may make any change in any option theretofore granted which adversely
affects the rights of any participant unless their consent is obtained. To the
extent necessary to comply with Section 423 of the Code (or any successor rule
or provision or any other applicable law, regulation or stock exchange rule),
the Company shall obtain stockholder approval of any amendment in such a manner
and to such a degree as required.

        (b)   Without stockholder approval and without regard to whether any
participant rights may be considered to have been "adversely affected," the
Administrator shall be entitled to change the Offering Periods, limit the
frequency and/or number of changes in the amount withheld during an Offering
Period, establish the exchange ratio applicable to amounts withheld in a
currency other than U.S. dollars, permit payroll withholding in excess of the
amount designated by a participant in order to adjust for delays or mistakes in
the Company's processing of properly completed withholding elections, establish
reasonable waiting and adjustment periods and/or accounting and crediting
procedures to ensure that amounts applied toward the purchase of Common Stock
for each participant properly correspond with amounts withheld from the
participant's Compensation, and establish such other limitations or procedures
as the Administrator determines in its sole discretion advisable which are
consistent with the Plan.

        (c)   Without regard to whether any participant's rights may be
considered to have been "adversely affected", in the event the Administrator
determines that the ongoing operation of the Plan may result in unfavorable
financial accounting consequences, the Board may, in its discretion

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and, to the extent necessary or desirable, modify or amend the Plan to reduce or
eliminate such accounting consequence including:

          (i)  increasing the Purchase Price for any Offering Period including
an Offering Period underway at the time of the change in Purchase Price;

         (ii)  shortening any Offering Period so that Offering Period ends on a
new Exercise Date, including an Offering Period underway at the time of the
Board action; and

        (iii)  reducing the number of shares that may be purchased upon exercise
of outstanding options.

        Such modifications or amendments shall not require stockholder approval
or the consent of any Plan participants.

        21.    Notices.    All notices or other communications by a participant
to the Company under or in connection with the Plan shall be deemed to have been
duly given when received in the form and manner specified by the Company at the
location, or by the person, designated by the Company for the receipt thereof.

        22.    Conditions Upon Issuance of Shares.    Shares shall not be issued
with respect to an option unless the exercise of such option and the issuance
and delivery of such shares pursuant thereto shall comply with all applicable
provisions of law, domestic or foreign, including, without limitation, the
Securities Act of 1933, as amended, the Exchange Act, the rules and regulations
promulgated thereunder, and the requirements of any stock exchange upon which
the shares may then be listed, and shall be further subject to the approval of
counsel for the Company with respect to such compliance.

        As a condition to the exercise of an option, the Company may require the
person exercising such option to represent and warrant at the time of any such
exercise that the shares are being purchased only for investment and without any
present intention to sell or distribute such shares if, in the opinion of
counsel for the Company, such a representation is required by any of the
aforementioned applicable provisions of law.

        23.    Term of Plan.    The Plan shall become effective upon the earlier
to occur of its adoption by the Board of Directors or its approval by the
stockholders of the Company. It shall continue in effect until the later of
(i) the date it is terminated under Section 20 hereof or (ii) the date which is
ten (10) years after the date such Plan is approved by the Board.

        24.    Stockholder Approval.    The Plan will be subject to approval by
the stockholders of the Company within twelve (12) months after the date the
Plan is adopted by the Board. Such stockholder approval will be obtained in the
manner and to the degree required under Applicable Laws.

9

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EXHIBIT A

OPTIMER PHARMACEUTICALS, INC.
EMPLOYEE STOCK PURCHASE PLAN
SUBSCRIPTION AGREEMENT

                         Original Application   Offering Date:
                                                 
                        
Change in Payroll Deduction Rate
 
 
 
                        
Change of Beneficiary(ies)
 
 
 

1.                                    hereby elects to participate in the
Optimer Pharmaceuticals, Inc. Employee Stock Purchase Plan (the "Employee Stock
Purchase Plan") and subscribes to purchase shares of Optimer
Pharmaceuticals, Inc.'s (the "Company") Common Stock in accordance with this
Subscription Agreement and the Employee Stock Purchase Plan.

2.I hereby authorize payroll deductions from each paycheck in the amount
of                        % of my Compensation on each pay day (from 0 to 10%)
during the Offering Period in accordance with the Employee Stock Purchase Plan.
(Please note that no fractional percentages are permitted.)

3.I understand that said payroll deductions shall be accumulated for the
purchase of shares of Common Stock at the applicable Purchase Price determined
in accordance with the Employee Stock Purchase Plan. I understand that if I do
not withdraw from an Offering Period, any accumulated payroll deductions will be
used to automatically exercise my option and purchase Common Stock under the
Employee Stock Purchase Plan.

4.I have received a copy of the complete Employee Stock Purchase Plan and its
accompanying prospectus. I understand that my participation in the Employee
Stock Purchase Plan is in all respects subject to the terms of the Plan.

5.Shares purchased for me under the Employee Stock Purchase Plan should be
issued in the name(s) of (Eligible Employee or Eligible Employee and
Spouse only).

6.I understand that if I dispose of any shares received by me pursuant to the
Employee Stock Purchase Plan within 2 years after the Offering Date (the first
day of the Offering Period during which I purchased such shares) or one year
after the Exercise Date, I will be treated for federal income tax purposes as
having received ordinary income at the time of such disposition in an amount
equal to the excess of the fair market value of the shares at the time such
shares were purchased by me over the price which I paid for the shares. I hereby
agree to notify the Company in writing within 30 days after the date of any
disposition of my shares and I will make adequate provision for Federal, state
or other tax withholding obligations, if any, which arise upon the disposition
of the Common Stock. The Company may, but will not be obligated to, withhold
from my compensation the amount necessary to meet any applicable withholding
obligation including any withholding necessary to make available to the Company
any tax deductions or benefits attributable to sale or early disposition of
Common Stock by me. If I dispose of such shares at any time after the expiration
of the 2-year and 1-year holding periods, I understand that I will be treated
for federal income tax purposes as having received income only at the time of
such disposition, and that such income will be taxed as ordinary income only to
the extent of an amount equal to the lesser of (1) the excess of the fair market
value of the shares at the time of such disposition over the purchase price
which I paid for the shares, or (2) 15% of the fair market value of the shares
on the first day of the Offering Period. The remainder of the gain, if any,
recognized on such disposition will be taxed as capital gain.

7.I hereby agree to be bound by the terms of the Employee Stock Purchase Plan.
The effectiveness of this Subscription Agreement is dependent upon my
eligibility to participate in the Employee Stock Purchase Plan.

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8.In the event of my death, I hereby designate the following as my
beneficiary(ies) to receive all payments and shares due me under the Employee
Stock Purchase Plan:

 
NAME: (Please print)
     

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(First)                                 (Middle)
                                (Last)

 

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Relationship
 

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Percentage of Benefit
 

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(Address)

 
NAME: (Please print)
     

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(First)                                 (Middle)
                                (Last)

 

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Relationship
 

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Percentage of Benefit
 

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(Address)

 
Employee's Social Security Number:
     

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Employee's Address:
 
 
 

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I UNDERSTAND THAT THIS SUBSCRIPTION AGREEMENT SHALL REMAIN IN EFFECT THROUGHOUT
SUCCESSIVE OFFERING PERIODS UNLESS TERMINATED BY ME.

Dated:
 
 
 
     

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Signature of Employee
 
 
 
 

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Spouse's Signature (If beneficiary other than spouse)

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EXHIBIT B

OPTIMER PHARMACEUTICALS, INC.
EMPLOYEE STOCK PURCHASE PLAN
NOTICE OF WITHDRAWAL

        The undersigned participant in the Offering Period of the Optimer
Pharmaceuticals, Inc. Employee Stock Purchase Plan that began
on                                    ,                         (the "Offering
Date") hereby notifies the Company that he or she hereby withdraws from the
Offering Period. He or she hereby directs the Company to pay to the undersigned
as promptly as practicable all the payroll deductions credited to his or her
account with respect to such Offering Period. The undersigned understands and
agrees that his or her option for such Offering Period will be automatically
terminated. The undersigned understands further that no further payroll
deductions will be made for the purchase of shares in the current Offering
Period and the undersigned shall be eligible to participate in succeeding
Offering Periods only by delivering to the Company a new Subscription Agreement.

 
 
Name and Address of Participant:
 
 

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    Signature:
 
 

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    Date:
 
 

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QuickLinks

OPTIMER PHARMACEUTICALS, INC. EMPLOYEE STOCK PURCHASE PLAN
EXHIBIT A OPTIMER PHARMACEUTICALS, INC. EMPLOYEE STOCK PURCHASE PLAN
SUBSCRIPTION AGREEMENT
EXHIBIT B OPTIMER PHARMACEUTICALS, INC. EMPLOYEE STOCK PURCHASE PLAN NOTICE OF
WITHDRAWAL