<PAGE>

                                                                 Exhibit 10.39

                            CHEMDEX CORPORATION
                            -------------------

                       1999 EMPLOYEE STOCK PURCHASE PLAN
                       ---------------------------------

     The following constitute the provisions of the 1999 Employee Stock Purchase
Plan of Chemdex Corporation:

     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. 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 shall, accordingly, be construed so as to extend and limit
participation in a manner consistent with the requirements of that section of
the Code.

     2.   Definitions.
          ------------

          (a)  "Board" means the Board of Directors of the Company.
                -----

          (b)  "Code" means the Internal Revenue Code of 1986, as amended.
                ----

          (c)  "Common Stock" means the Common Stock of the Company.
                ------------

          (d)  "Company" means Chemdex Corporation, a Delaware corporation.
                -------

          (e) "Compensation" means total cash compensation received by an
               ------------
Employee from the Company or a Designated Subsidiary. By way of illustration,
but not limitation, Compensation includes regular compensation such as salary,
wages, overtime, shift differentials, bonuses, commissions and incentive
compensation, but excludes relocation, expense reimbursements, tuition or other
reimbursements and income realized as a result of participation in any stock
option, stock purchase, or similar plan of the Company or any Designated
Subsidiary.

          (f) "Continuous Status as an Employee" means the absence of any
               --------------------------------
interruption or termination of service as an Employee. Continuous Status as an
Employee shall not be considered interrupted in the case of (i) sick leave; (ii)
military leave; (iii) any other leave of absence approved by the Administrator,
provided that such leave is for a period of not more than 90 days, unless
reemployment upon the expiration of such leave is guaranteed by contract or
statute, or unless provided otherwise pursuant to Company policy adopted from
time to time; or (iv) in the case of transfers between locations of the Company
or between the Company and its Designated Subsidiaries.

          (g) "Contributions" means all amounts credited to the account of a
               -------------
participant pursuant to the Plan.

          (h) "Corporate Transaction" means a sale of all or substantially all
               ---------------------
of the Company's assets, or a merger, consolidation or other capital
reorganization of the Company with or into another corporation, or any other
transaction or series of related transactions in
<PAGE>

which the Company's stockholders immediately prior thereto own less than 50% of
the voting stock of the Company (or its successor or parent) immediately
thereafter.

          (i) "Designated Subsidiaries" means the Subsidiaries that have been
               -----------------------
designated by the Board from time to time in its sole discretion as eligible to
participate in the Plan; provided however that the Board shall only have the
discretion to designate Subsidiaries if the issuance of options to such
Subsidiary's Employees pursuant to the Plan would not cause the Company to incur
adverse accounting charges.

          (j) "Employee" means any person, including an Officer, who is an
               --------
Employee for tax purposes and who is customarily employed for at least twenty
(20) hours per week and more than five (5) months in a calendar year by the
Company or one of its Designated Subsidiaries.

          (k) "Exchange Act" means the Securities Exchange Act of 1934, as
               ------------
amended.

          (1) "Offering Date" means the first business day of each Offering
               -------------
Period of the Plan.

          (m) "Offering Period" means a period of twenty-four (24) months
               ---------------
commencing on February 16 and August 16 of each year, except for the first
Offering Period as set forth in Section 4(a).

          (n) "Officer" means a person who is an officer of the Company within
               -------
the meaning of Section 16 of the Exchange Act and the rules and regulations
promulgated thereunder.

          (o)  "Plan" means this Employee Stock Purchase Plan.
                ----

          (p) "Purchase Date" means the last day of each Purchase Period of the
               -------------
Plan.

          (q) "Purchase Period" means a period of six (6) months within an
               ---------------
Offering Period, except as set forth in Section 4(b).

          (r) "Purchase Price" means with respect to a Purchase Period an amount
               --------------
equal to 85% of the Fair Market Value (as defined in Section 7(b) below) of a
Share of Common Stock on the Offering Date or on the Purchase Date, whichever is
lower; provided, however, that in the event (i) of any increase in the number of
Shares available for issuance under the Plan as a result of a stockholder-
approved amendment to the Plan, and (ii) all or a portion of such additional
Shares are to be issued with respect to one or more Offering Periods that are
underway at the time of such increase ("Additional Shares"), and (iii) the Fair
                                        -----------------
Market Value of a Share of Common Stock on the date of such increase (the

"Approval Date Fair Market Value") is higher than the Fair Market Value on the
--------------------------------
Offering Date for any such Offering Period, then in such instance the Purchase
Price with respect to Additional Shares shall be 85% of the Approval Date Fair
Market Value or the Fair Market Value of a Share of Common Stock on the Purchase
Date, whichever is lower.

                                      -2-
<PAGE>

          (s) "Share" means a share of Common Stock, as adjusted in accordance
               -----
with Section 19 of the Plan.

          (t) "Subsidiary" means a corporation, domestic or foreign, of which
               ----------
not less than 50% of the voting shares are held by the Company or a Subsidiary,
whether or not such corporation now exists or is hereafter organized or acquired
by the Company or a Subsidiary.

     3.   Eligibility.
          -----------

          (a) Any person who is an Employee as of the Offering Date of a given
Offering Period shall be eligible to participate in such Offering Period under
the Plan, subject to the requirements of Section 5(a) and the limitations
imposed by Section 423(b) of the Code; provided however that eligible Employees
may not participate in more than one Offering Period at a time.

          (b) Any provisions of the Plan to the contrary notwithstanding, no
Employee shall be granted an option under the Plan (i) if, immediately after the
grant, such Employee (or any other person whose stock would be attributed to
such Employee pursuant to Section 424(d) of the Code) would own capital stock of
the Company and/or hold outstanding options to purchase stock possessing five
percent (5%) or more of the total combined voting power or value of all classes
of stock of the Company or of any subsidiary of the Company, or (ii) if such
option would permit his or her rights to purchase stock under all employee stock
purchase plans (described in Section 423 of the Code) of the Company and its
Subsidiaries to accrue at a rate that exceeds Twenty-Five Thousand Dollars
($25,000) of the Fair Market Value (as defined in Section 7(b) below) of such
stock (determined at the time such option is granted) for each calendar year in
which such option is outstanding at any time.

     4.   Offering Periods and Purchase Periods.
          --------------------------------------

          (a) Offering Periods. The Plan shall be generally implemented by a
              ----------------
series of Offering Periods of twenty-four (24) months' duration, with new
Offering Periods (other than the first Offering Period) commencing on or about
February 16 and August 16 of each year (or at such other time or times as may be
determined by the Board of Directors). The first Offering Period shall commence
on the beginning of the effective date of the Registration Statement on Form S-1
for the initial public offering of the Company's Common Stock (the "IPO Date")
                                                                    --------
and continue until August 15, 2001. The Plan shall continue until terminated in
accordance with Section 19 hereof. The Board of Directors of the Company shall
have the power to change the duration and/or the frequency of Offering Periods
with respect to future offerings without stockholder approval if such change is
announced at least five (5) days prior to the scheduled beginning of the first
Offering Period to be affected.

          (b) Purchase Periods. Each Offering Period shall generally consist of
              ----------------
four (4) consecutive purchase periods of six (6) months' duration. The last day
of each Purchase Period shall be the "Purchase Date" for such Purchase Period. A
                                      -------------
Purchase Period commencing on February 16 shall end on the next August 15. A
Purchase Period commencing on August 16 shall end on the next February 15. The
first Purchase Period of the first Offering Period shall

                                      -3-
<PAGE>

commence on the IPO Date and shall end on February 15, 2000. The Board of
Directors of the Company shall have the power to change the duration and/or
frequency of Purchase Periods with respect to future purchases without
stockholder approval if such change is announced at least five (5) days prior to
the scheduled beginning of the first Purchase Period to be affected.

     5.   Participation.
          --------------

          (a) An eligible Employee may become a participant in the Plan by
completing a subscription agreement on the form provided by the Company and
filing it with the Company's payroll office or the stock brokerage or other
financial services firm designated by the Company (the "Designated Broker")
prior to the applicable Offering Date, unless a later time for filing the
subscription agreement is set by the Board for all eligible Employees with
respect to a given Offering Period. The subscription agreement shall set forth
the percentage of the participant's Compensation (subject to Section 6(a) below)
to be paid as Contributions pursuant to the Plan.

          (b) Payroll deductions shall commence on the first payroll paid after
the Offering Date and shall end on the last payroll paid on or prior to the last
Purchase Period of the Offering Period to which the subscription agreement is
applicable, unless sooner terminated by the participant as provided in Section
10.

     6.   Method of Payment of Contributions.
          -----------------------------------

          (a) A participant shall elect to have payroll deductions made on each
payday during the Offering Period in an amount not less than one percent (1%)
and not more than twenty percent (20%) (or such other percentage as the Board
may establish from time to time before an Offering Date) of such participant's
Compensation on each payday during the Offering Period. All payroll deductions
made by a participant shall be credited to his or her account under the Plan. A
participant may not make any additional payments into such account.

          (b) A participant may discontinue his or her participation in the Plan
as provided in Section 10, or may increase or decrease the rate of his or her
Contributions by completing and filing with the Company or its Designated Broker
a new subscription agreement authorizing a change in the payroll deduction rate.
The Board may, in its discretion, limit the number of rate changes during any
Offering Period. The change in rate shall be effective with the first full
payroll following five (5) business days after the Company's receipt of the new
subscription agreement, unless the Company elects to process a given rate change
more quickly. A participant's subscription agreement shall remain in effect for
successive Offering Periods unless terminated as provided in Section 10.

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

                                      -4-
<PAGE>

     7.   Grant of Option.
          ---------------

          (a) 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 Purchase Date a number of Shares of the Company's Common Stock
determined by dividing such Employee's Contributions accumulated prior to such
Purchase Date and retained in the participant's account as of the Purchase Date
by the applicable Purchase Price; provided however that the maximum number of
Shares an Employee may purchase during each Purchase Period shall be 1,250
Shares (subject to any adjustment pursuant to Section 19 below), and provided
further that such purchase shall be subject to the limitations set forth in
Sections 3(b) and 13.

          (b) The fair market value of the Company's Common Stock on a given
date (the "Fair Market Value") shall be determined by the Board in its
           -----------------
discretion based on the closing sales price of the Common Stock for such date
(or, in the event that the Common Stock is not traded on such date, on the
immediately preceding trading date), as reported by the National Association of
Securities Dealers Automated Quotation (Nasdaq) National Market or, if such
price is not reported, the mean of the bid and asked prices per share of the
Common Stock as reported by Nasdaq or, in the event the Common Stock is listed
on a stock exchange, the Fair Market Value per share shall be the closing sales
price on such exchange on such date (or, in the event that the Common Stock is
not traded on such date, on the immediately preceding trading date), as reported
in The Wall Street Journal. For purposes of the Offering Date under the first
   -----------------------
Offering Period under the Plan, the Fair Market Value of a share of the Common
Stock of the Company shall be the Price to Public as set forth in the final
prospectus filed with the Securities and Exchange Commission pursuant to Rule
424 under the Securities Act of 1933, as amended.

     8.  Exercise of Option. Unless a participant withdraws from the Plan as
         ------------------
provided in Section 10, his or her option for the purchase of Shares will be
exercised automatically on each Purchase Date of an Offering Period, and the
maximum number of full Shares subject to the option will be purchased at the
applicable Purchase Price with the accumulated Contributions in his or her
account. No fractional Shares shall be issued; any payroll deductions
accumulated in a participant's account that are not sufficient to purchase a
full Share shall be retained in the participant's account for the subsequent
Purchase Period or Offering Period, subject to earlier withdrawal by the
participant as provided in Section 10 below. Any other amounts left over in a
participant's account after a Purchase Date shall be returned to the
participant. During his or her lifetime, a participant's option to purchase
Shares hereunder is exercisable only by him or her.

     9.  Delivery. As promptly as practicable after each Purchase Date of each
         --------
Offering Period, the number of Shares purchased by each participant upon
exercise of his or her option shall be deposited into an account established in
the participant's name with the Designated Broker.

     10.  Voluntary Withdrawal; Termination of Employment.
          -----------------------------------------------

          (a) A participant may withdraw all but not less than all the
Contributions credited to his or her account under the Plan at any time prior
to each Purchase Date by giving written notice to the Company or the
Designated Broker, as directed by the Company. All of the
                                      -5-
<PAGE>

participant's Contributions credited to his or her account will be paid to him
or her promptly after receipt of his or her notice of withdrawal and his or
her option for the current period will be automatically terminated, and no
further Contributions for the purchase of Shares will be made during the
Offering Period.

          (b) Upon termination of the participant's Continuous Status as an
Employee prior to the Purchase Date of an Offering Period for any reason,
including retirement or death, the Contributions credited to his or her account
will be returned to him or her or, in the case of his or her death, to the
person or persons entitled thereto under Section 14, and his or her option will
be automatically terminated.

          (c) In the event an Employee fails to remain in Continuous Status as
an Employee of the Company for at least twenty (20) hours per week during the
Offering Period in which the employee is a participant, he or she will be deemed
to have elected to withdraw from the Plan and the Contributions credited to his
or her account will be returned to him or her and his or her option terminated.

          (d) A participant's withdrawal from an offering will not have any
effect upon his or her eligibility to participate in a succeeding offering or in
any similar plan that may hereafter be adopted by the Company.

     11.  Automatic Withdrawal. If the Fair Market Value of the Shares on any
          --------------------
Purchase Date of an Offering Period is less than the Fair Market Value of the
Shares on the Offering Date for such Offering Period, then every participant
shall automatically (i) be withdrawn from such Offering Period at the close of
such Purchase Date and after the acquisition of Shares for such Purchase Period,
and (ii) be enrolled in the Offering Period commencing on the first business day
subsequent to such Purchase Period. Participants shall automatically be
withdrawn as of August 15, 1999 from the Offering Period beginning on the IPO
Date and re-enrolled in the Offering Period beginning on August 16, 1999 if the
Fair Market Value of the Shares on the IPO Date is greater than the Fair Market
Value of the Shares on August 15, 1999, unless a participant notifies the
Administrator prior to August 15, 1999 that he or she does not wish to be
withdrawn and re-enrolled.

     12.  Interest. No interest shall accrue on the Contributions of a
          --------
     participant in the
Plan.

     13.  Stock.
          -----

          (a) Subject to adjustment as provided in Section 19, the maximum
number of Shares which shall be made available for sale under the Plan shall
be 750,000 Shares, plus an automatic annual increase on the first day of each
of the Company's fiscal years beginning in 2000, 2001, 2002, 2003 and 2004
equal to the lesser of (i) 200,000 Shares, (ii) one-half of one percent (.5%)
of the Shares outstanding on the last day of the immediately preceding fiscal
year or (iii) a lesser amount determined by the Board. If the Board determines
that, on a given Purchase 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

                                      -6-
<PAGE>

on the Offering Date of the applicable Offering Period, or (ii) the number of
shares available for sale under the Plan on such Purchase Date, the Board may
in its sole discretion provide (x) that the Company shall make a pro rata
allocation of the Shares of Common Stock available for purchase on such
Offering Date or Purchase Date, as applicable, 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 Purchase Date, and continue all Offering Periods then in effect, or
(y) that the Company shall make a pro rata allocation of the shares available
for purchase on such Offering Date or Purchase Date, as applicable, 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 Purchase Date, and terminate any or all Offering
Periods then in effect pursuant to Section 20 below. The Company may make 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.

          (b) The participant shall have no interest or voting right in Shares
covered by his or her option until such option has been exercised.

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

     14.  Administration. The Board, or a committee named by the Board, shall
          --------------
supervise and administer the Plan and shall have full power to adopt, amend and
rescind any rules deemed desirable and appropriate for the administration of the
Plan and not inconsistent with the Plan, to construe and interpret the Plan, and
to make all other determinations necessary or advisable for the administration
of the Plan.

     15.  Designation of Beneficiary.
          --------------------------

          (a) A participant may file a written 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 the end of a
Purchase Period but prior to delivery to him or her of such Shares and cash. In
addition, a participant may file a written 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 the Purchase Date of an Offering Period. 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 (and his or her spouse, if any) at any time by written notice. 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 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,

                                      -7-
<PAGE>

or if no spouse, dependent or relative is known to the Company, then to such
other person as the Company may designate.

     16.  Transferability. Neither Contributions 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) 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 in
accordance with Section 10.

     17.  Use of Funds. All Contributions 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 Contributions.

     18.  Reports. Individual accounts will be maintained for each participant
          -------
in the Plan. Statements of account will be given to participating Employees at
least annually, which statements will set forth the amounts of Contributions,
the per Share Purchase Price, the number of Shares purchased and the remaining
cash balance, if any.

      19.  Adjustments Upon Changes in Capitalization; Corporate Transactions.
            ------------------------------------------------------------------

           (a) Adjustment. Subject to any required action by the stockholders of
               ----------
the Company, the number of Shares covered by each option under the Plan that has
not yet been exercised and the number of Shares that have been authorized for
issuance under the Plan but have not yet been placed under option (collectively,
the "Reserves"), as well as the maximum number of shares of Common Stock that
may be purchased by a participant in a Purchase Period, the number of shares of
Common Stock set forth in Section 13(a)(i) above, and the price per Share of
Common Stock covered by each option under the Plan that has not yet been
exercised, shall be proportionately adjusted for any increase or decrease in the
number of issued Shares resulting from a stock split, reverse stock split, stock
dividend, combination or reclassification of the Common Stock (including any
such change in the number of Shares of Common Stock effected in connection with
a change in domicile of the Company), or any other increase or decrease in the
number of Shares 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 Board, whose determination in that respect
shall be final, binding and conclusive. Except as expressly provided herein, no
issue 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 subject to
an option.

          (b) Corporate Transactions. In the event of a dissolution or
              ----------------------
liquidation of the Company, any Purchase Period and Offering Period then in
progress will terminate immediately prior to the consummation of such action,
unless otherwise provided by the Board. In the event of a Corporate
Transaction, each option outstanding under the Plan shall be assumed or an
equivalent option shall be substituted by the successor corporation or a
parent or Subsidiary of such successor corporation. In the event that the
successor corporation refuses to assume or
                                      -8-
<PAGE>

substitute for outstanding options each Purchase Perio d and Offering Period
then in progress shall be shortened and a new Purchase Date shall be set (the
"New Purchase Date"), as of which date any Purchase Period and Offe ring Period
 -----------------
then in progress will terminate. The New Purchase Date shall be on or before the
date of consummation of the transaction and the Board shall notify each
participant in writing, at least ten (10) days prior to the New Purchase Date,
that the Purchase Date for his or her option has been changed to the New
Purchase Date and that his or her option will be exercised automatically on the
New Purchase Date, unless prior to such date he or she has withdrawn from the
Offering Period as provided in Section 10. For purposes of this Section 19, an
option granted under the Plan shall be deemed to be assumed, without limitation,
if, at the time of issuance of the stock or other consideration upon a Corporate
Transaction, each holder of an option under the Plan would be entitled to
receive upon exercise of the option the same number and kind of shares of stock
or the same amount of property, cash or securities as such holder would have
been entitled to receive upon the occurrence of the transaction if the holder
had been, immediately prior to the transaction, the holder of the number of
Shares of Common Stock covered by the option at such time (after giving effect
to any adjustments in the number of Shares covered by the option as provided for
in this Section 19); provided however that if the consideration received in the
transaction is not solely common stock of the successor corporation or its
parent (as defined in Section 424(e) of the Code), the Board may, with the
consent of the successor corporation, provide for the consideration to be
received upon exercise of the option to be solely common stock of the successor
corporation or its parent equal in Fair Market Value to the per Share
consideration received by holders of Common Stock in the transaction.

     The Board may, if it so determines in the exercise of its sole discretion,
also make provision for adjusting the Reserves, as well as the price per Share
of Common Stock covered by each outstanding option, in the event that the
Company effects one or more reorganizations, recapitalizations, rights offerings
or other increases or reductions of Shares of its outstanding Common Stock, and
in the event of the Company's being consolidated with or merged into any other
corporation.

     20.  Amendment or Termination.
          ------------------------

          (a) The Board may at any time and for any reason terminate or amend
the Plan. Except as provided in Section 19, no such termination of the Plan may
affect options previously granted, provided that the Plan or an Offering Period
may be terminated by the Board on a Purchase Date or by the Board's setting a
new Purchase Date with respect to an Offering Period and Purchase Period then in
progress if the Board determines that termination of the Plan and/or the
Offering Period is in the best interests of the Company and the stockholders or
if continuation of the Plan and/or the Offering Period would cause the Company
to incur adverse accounting charges as a result of a change after the effective
date of the Plan in the generally accepted accounting rules applicable to the
Plan. Except as provided in Section 19 and in this Section 20, no amendment to
the Plan shall make any change in any option previously granted that adversely
affects the rights of any participant. In addition, to the extent necessary to
comply with Rule 16b-3 under the Exchange Act, or under Section 423 of the Code
(or any successor rule or provision or any applicable law or regulation), the
Company shall obtain stockholder approval in such a manner and to such a degree
as so required.

                                      -9-
<PAGE>

          (b) Without stockholder consent and without regard to whether any
participant rights may be considered to have been adversely affected, the Board
(or its committee) shall be entitled to change the Offering Periods and Purchase
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 Board (or its committee) determines in its sole discretion
advisable that are consistent with the Plan.

     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 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, applicable state securities laws 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; Effective Date. The Plan shall become effective upon the
          ----------------------------
IPO Date. It shall continue in effect for a term of twenty (20) years unless
sooner terminated under Section 20.

     24.  Additional Restrictions of Rule 16b-3. The terms and conditions of
          -------------------------------------
options granted hereunder to, and the purchase of Shares by, persons subject to
Section 16 of the Exchange Act shall comply with the applicable provisions of
Rule 16b-3. This Plan shall be deemed to contain, and such options shall
contain, and the Shares issued upon exercise thereof shall be subject to, such
additional conditions and restrictions as may be required by Rule 16b-3 to
qualify for the maximum exemption from Section 16 of the Exchange Act with
respect to Plan transactions.

                                      -10-
<PAGE>

                               CHEMDEX CORPORATION

                        1999 EMPLOYEE STOCK PURCHASE PLAN
                              SUBSCRIPTION AGREEMENT
                              ----------------------



                                                             New Election
                                                                         ------
                                                       Change of Election
                                                                         ------


      1.   I,                     , hereby elect to participate in the Chemdex
             ---------------------
Corporation 1999 Employee Stock Purchase Plan (the "Plan") for the Offering
Period               ,     to             ,   , and subscribe to purchase
       --------------  ---    ------------ ---
shares of the Company's Common Stock in Accordance with this Subscription
Agreement and the Plan.

      2.   I elect to have Contributions in the amount of     % of my
                                                          ----
Compensation, as those terms are defined in the plan, applied to this
purchase. I understand that this amount must not be less than 1% and not more
than 20% of my Compensation during the Offering Period. (Please note that no
fractional percentages are permitted).

      3.   I hereby authorize payroll deductions from each paycheck during the
Offering Period at the rate stated in Item 2 of this Subscription Agreement. I
understand that all payroll deductions made by me shall be credited to my
account under the Plan and that I may not make any additional payments into
such account. I understand that all payments made by me shall be accumulated
for the purchase of shares of Common Stock at the applicable purchase price
determined in accordance with the Plan. I further understand that, except as
otherwise set forth in the plan, shares will be purchased for me automatically
on the Purchase Date of each Offering Period unless I otherwise withdraw from
the plan by giving written notice to the Company for such purpose.

      4.   I understand that I may discontinue at any time prior to the
Purchase Date my participation in the Plan as provided in Section 10 of the
plan. I also understand that, unless otherwise provided by the Plan
administrator, I can increase or decrease the rate of my Contributions during
a Purchase Period, other than the first Purchase Period as follows: 1) I can
increase the rate of my Contributions for a Purchase Period, other than the
first Purchase Period of an Offering Period, by completing and filing a new
subscription Agreement at least five (5) business days prior to the first day
of the applicable Purchase Period, with such rate change taking effect on the
first day of such Purchase Period; and 2) I can decrease the rate of my
Contributions on one occasion only during a Purchase Period, by completing and
filing a new Subscription Agreement, with such rate change taking effect with
the first full payroll following five (5) business days after the Company;s
receipt of the new Subscription Agreement. Further, I may change the rate of
deductions for future Offerings Periods by filling a new Subscription
Agreement, and any such change will be effective as of the beginning of the
next Offering Period. In addition, I

<PAGE>

acknowledge that, unless I discontinue my participation in the Plan as
provided in Section 10 of the Plan, my election will continue to be effective
for each successive Offering Period.

      5.   I have received a copy of the Company's most recent description of
the Plan and a copy of the complete "Chemdex Corporation 1999 Employee Stock
Purchase Plan." I understand that my participation in the Plan is in all
respects subject to the terms of the Plan.

      6.   Shares purchased for me under the plan should be issued in the
name(s) of (name of employee and spouse only):

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

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

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


Name: (Please print)                           ------------------------------
                                               (First)    (Middle)   (Last)


------------------------                       ------------------------------
(Relationship)                                 (Address)


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

      8.   I understand that if I dispose of any shares received by me
pursuant to the Plan within 2 years after the Offering Date (the first day of
the Offering Period during which I purchased such shares) or within 1 year
after the Purchase Date, I will be treated for federal income tax purposes as
having received ordinary compensation income at the time of such disposition
in an amount equal to the excess of the fair market value of the shares on the
Purchase Date over the price that I paid for the shares, regardless of whether
I disposed of the shares at a price less than their fair market value at the
Purchase Date. The remainder of the gain or loss, if any, recognized on such
disposition will be treated as capital gain or loss.

      I hereby agree to notify the Company in writing within 30 days after the
      ------------------------------------------------------------------------
date of any such disposition, and I will make adequate provision for federal,
-----------------------------------------------------------------------------
state or other tax withholding obligations, if any, that 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 the sale or early
disposition of Common Stock by me.

      9.   If I dispose of such shares at any time after expiration of the
2-year and 1-year holding periods, I understand that I will be treated for
federal income tax purposes as having

                                     -2-
<PAGE>

received compensation 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 that I paid for the shares under the
option, or (2) 15% of the fair market value of the shares on the Offering
Date. The remainder of the gain or loss, if any, recognized on such
disposition will be treated as capital gain or loss.

      I understand that this tax summary is only a summary and is subject to
      ----------------------------------------------------------------------
change. I further understand that I should consult a tax advisor concerning the
------
tax implications of the purchase and sale of the stock under the plan.

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



SIGNATURE:
          ----------------------------------


SOCIAL SECURITY #:
                  --------------------------


DATE:
     ---------------------------------------




SPOUSE'S SIGNATURE(necessary
if beneficiary is not spouse):


--------------------------------------------
(Signature)



--------------------------------------------
(Print Name)








                                     -3-
<PAGE>

                              CHEMDEX CORPORATION

                       1999 EMPLOYEE STOCK PURCHASE PLAN

                              NOTICE OF WITHDRAWAL
                              --------------------


     I,                     , hereby elect to withdraw my participation in the
       ---------------------
Chemdex Corporation 1999 Employee Stock Purchase plan (the "Plan") for the
                                                            ----
offering Period that began on                    ,       . This withdrawal
                              ------------- -----  ------
covers all Contributions credited to my account and is effective on the date
designated below.

     I understand that all Contributions credited to my account will be paid to
me within ten (10) business days of receipt by the Company of this Notice of
Withdrawal and that my option purchase of shares can be made by me during the
Offering Period.

     The undersigned further understands and agrees that he or she shall be
eligible to participate in succeeding offering periods only by delivering to
the Company a new Subscription Agreement.


Dated:
      ---------------------              ----------------------------------
                                         Signature of Employee


                                         ----------------------------------
                                         Social Security Number
















                                     -4-