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                                                                   EXHIBIT 10.60

                                SEQUENOM, INC.

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


     I.   PURPOSE OF THE PLAN

          This Employee Stock Purchase Plan is intended to promote the interests
of Sequenom, Inc., a Delaware corporation, by providing eligible employees with
the opportunity to acquire a proprietary interest in the Corporation through
participation in a payroll deduction-based employee stock purchase plan designed
to qualify under Section 423 of the Code.

          Capitalized terms herein shall have the meanings assigned to such
terms in the attached Appendix.

     II.  ADMINISTRATION OF THE PLAN

          The Plan Administrator shall have full authority to interpret and
construe any provision of the Plan and to adopt such rules and regulations for
administering the Plan as it may deem necessary in order to comply with the
requirements of Code Section 423. Decisions of the Plan Administrator shall be
final and binding on all parties having an interest in the Plan.

     III. STOCK SUBJECT TO PLAN

          A.   The stock purchasable under the Plan shall be shares of
authorized but unissued or reacquired Common Stock, including shares of Common
Stock purchased on the open market. The number of shares of Common Stock
initially reserved for issuance over the term of the Plan shall be limited to
250,000 shares.

          B.   The number of shares of Common Stock available for issuance under
the Plan shall automatically increase on the first trading day of January each
calendar year during the term of the Plan, beginning with calendar year 2001, by
an amount equal to one percent (1%) of the total number of shares of Common
Stock outstanding on the last trading day in December of the immediately
preceding calendar year, but in no event shall any such annual increase exceed
500,000 shares.

          C.   Should any change be made to the Common Stock by reason of any
stock split, stock dividend, recapitalization, combination of shares, exchange
of shares or other change affecting the outstanding Common Stock as a class
without the Corporation's receipt of consideration, appropriate adjustments
shall be made to (i) the maximum number and class of securities issuable under
the Plan, (ii) the maximum number and class of securities purchasable per
Participant on any one Purchase Date, (iii) the maximum number and class of
securities purchasable in total by all Participants on any one Purchase Date,
(iv) the maximum number
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and/or class of securities by which the share reserve is to increase
automatically each calendar year pursuant to the provisions of Section III.B of
this Article One and (v) the number and class of securities and the price per
share in effect under each outstanding purchase right in order to prevent the
dilution or enlargement of benefits thereunder.

     IV.  OFFERING PERIODS

          A.   Shares of Common Stock shall be offered for purchase under the
Plan through a series of overlapping offering periods until such time as (i) the
maximum number of shares of Common Stock available for issuance under the Plan
shall have been purchased or (ii) the Plan shall have been sooner terminated.

          B.   Each offering period shall be of such duration (not to exceed
twenty-four (24) months) as determined by the Plan Administrator prior to the
start date of such offering period. Offering periods shall commence at
semi-annual intervals on the first business day of February and August each year
over the term of the Plan. Accordingly, two (2) separate offering periods shall
commence in each calendar year the Plan remains in existence. However, the
initial offering period shall commence at the Effective Time and terminate on
the last business day in January 2002.

          C.   Each offering period shall consist of a series of one or more
successive Purchase Intervals. Purchase Intervals shall run from the first
business day in February to the last business day in July each year and from the
first business day in August each year to the last business day in January in
the following year. However, the first Purchase Interval in effect under the
initial offering period shall commence at the Effective Time and terminate on
the last business day in July 2000.

          D.   Should the Fair Market Value per share of Common Stock on any
Purchase Date within a particular offering period be less than the Fair Market
Value per share of Common Stock on the start date of that offering period, then
that offering period shall automatically terminate immediately after the
purchase of shares of Common Stock on such Purchase Date, and a new offering
period shall commence on the next business day following such Purchase Date. The
new offering period shall have a duration of twenty (24) months, unless a
shorter duration is established by the Plan Administrator within five (5)
business days following the start date of that offering period. All individuals
participating in the terminated offering period shall automatically be
transferred to the new offering period.

     V.   ELIGIBILITY

          A.   Each individual who is an Eligible Employee on the start date of
any offering period under the Plan may enter that offering period on such start
date. However, an Eligible Employees may participate in only one offering period
at a time.

                                       2.
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          B.   Except as provided in Section IV.D. above, an Eligible Employee
must, in order to participate in a particular offering period, complete the
enrollment forms prescribed by the Plan Administrator (including a stock
purchase agreement and a payroll deduction authorization) and file such forms
with the Plan Administrator (or its designate) on or before the start date of
that offering period.

     VI.  PAYROLL DEDUCTIONS

          A.   The payroll deduction authorized by the Participant for purposes
of acquiring shares of Common Stock during an offering period may be any
multiple of one percent (1%) of the Base Salary paid to the Participant during
each Purchase Interval within that offering period, up to a maximum of fifteen
percent (15%). The deduction rate so authorized shall continue in effect
throughout the offering period, except to the extent such rate is changed in
accordance with the following guidelines:

               (i)  The Participant may, at any time during the offering period,
     reduce his or her rate of payroll deduction to become effective as soon as
     possible after filing the appropriate form with the Plan Administrator. The
     Participant may not, however, effect more than one (1) such reduction per
     Purchase Interval.

               (ii) The Participant may, prior to the commencement of any new
     Purchase Interval within the offering period, increase the rate of his or
     her payroll deduction by filing the appropriate form with the Plan
     Administrator. The new rate (which may not exceed the fifteen percent (15%)
     maximum) shall become effective on the start date of the first Purchase
     Interval following the filing of such form.

          B.   Payroll deductions shall begin on the first pay day
administratively feasible following the Participant's Entry Date into the
offering period and shall (unless sooner terminated by the Participant) continue
through the pay day ending with or immediately prior to the last day of that
offering period. The amounts so collected shall be credited to the Participant's
book account under the Plan, but no interest shall be paid on the balance from
time to time outstanding in such account. The amounts collected from the
Participant shall not be required to be held in any segregated account or trust
fund and may be commingled with the general assets of the Corporation and used
for general corporate purposes.

          C.   Payroll deductions shall automatically cease upon the termination
of the Participant's purchase right in accordance with the provisions of the
Plan.

          D.   The Participant's acquisition of Common Stock under the Plan on
any Purchase Date shall neither limit nor require the Participant's acquisition
of Common Stock on any subsequent Purchase Date, whether within the same or a
different offering period.

                                       3.
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     VII.  PURCHASE RIGHTS

           A.  Grant of Purchase Rights.  A Participant shall be granted a
               ------------------------
separate purchase right for each offering period in which he or she
participates. The purchase right shall be granted on the start date of the
offering period and shall provide the Participant with the right to purchase
shares of Common Stock, in a series of successive installments during that
offering period, upon the terms set forth below. The Participant shall execute a
stock purchase agreement embodying such terms and such other provisions (not
inconsistent with the Plan) as the Plan Administrator may deem advisable.

           Under no circumstances shall purchase rights be granted under the
Plan to any Eligible Employee if such individual would, immediately after the
grant, own (within the meaning of Code Section 424(d)) or hold outstanding
options or other rights to purchase, stock possessing five percent (5%) or more
of the total combined voting power or value of all classes of stock of the
Corporation or any Corporate Affiliate.

           B.  Exercise of the Purchase Right. Each purchase right shall be
               ------------------------------
automatically exercised in installments on each successive Purchase Date within
the offering period, and shares of Common Stock shall accordingly be purchased
on behalf of each Participant on each such Purchase Date. The purchase shall be
effected by applying the Participant's payroll deductions for the Purchase
Interval ending on such Purchase Date to the purchase of whole shares of Common
Stock at the purchase price in effect for the Participant for that Purchase
Date.

           C.  Purchase Price.  The purchase price per share at which Common
               --------------
Stock will be purchased on the Participant's behalf on each Purchase Date within
the particular offering period in which he or she is participating shall be
equal to eighty-five percent (85%) of the lower of (i) the Fair Market Value per
share of Common Stock on the start date of that offering period or (ii) the Fair
Market Value per share of Common Stock on that Purchase Date.

           D.  Number of Purchasable Shares.  The number of shares of Common
               ----------------------------
Stock purchasable by a Participant on each Purchase Date during the particular
offering period in which he or she is participating shall be the number of whole
shares obtained by dividing the amount collected from the Participant through
payroll deductions during the Purchase Interval ending with that Purchase Date
by the purchase price in effect for the Participant for that Purchase Date.
However, the maximum number of shares of Common Stock purchasable per
Participant on any one Purchase Date shall not exceed 1,000 shares, subject to
periodic adjustments in the event of certain changes in the Corporation's
capitalization. In addition, the maximum number of shares of Common Stock
purchasable in total by all Participants on any one Purchase Date shall not
exceed 62,500 shares, subject to periodic adjustments in the event of certain
changes in the Corporation's capitalization. However, the Plan Administrator
shall have the discretionary authority, exercisable prior to the start of any
offering period under the Plan, to increase or decrease the limitations to be in
effect for the number of shares purchasable per Participant and in total by all
Participants on each Purchase Date during that offering period.

                                       4.
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          E.   Excess Payroll Deductions.  Any payroll deductions not applied to
               -------------------------
the purchase of shares of Common Stock on any Purchase Date because they are not
sufficient to purchase a whole share of Common Stock shall be held for the
purchase of Common Stock on the next Purchase Date. However, any payroll
deductions not applied to the purchase of Common Stock by reason of the
limitation on the maximum number of shares purchasable per Participant or in
total by all Participants on the Purchase Date shall be promptly refunded.

          F.   Termination of Purchase Right.  The following provisions shall
               -----------------------------
govern the termination of outstanding purchase rights:

               (i)   A Participant may, at any time prior to the next scheduled
     Purchase Date in the offering period in which he or she is participating,
     terminate his or her outstanding purchase right by filing the appropriate
     form with the Plan Administrator (or its designate), and no further payroll
     deductions shall be collected from the Participant with respect to the
     terminated purchase right. Any payroll deductions collected during the
     Purchase Interval in which such termination occurs shall, at the
     Participant's election, be immediately refunded or held for the purchase of
     shares on the next Purchase Date. If no such election is made at the time
     such purchase right is terminated, then the payroll deductions collected
     with respect to the terminated right shall be refunded as soon as possible.

               (ii)  The termination of such purchase right shall be
     irrevocable, and the Participant may not subsequently rejoin the offering
     period for which the terminated purchase right was granted. In order to
     resume participation in any subsequent offering period, such individual
     must re-enroll in the Plan (by making a timely filing of the prescribed
     enrollment forms) on or before the start date of that offering period.

               (iii) Should the Participant cease to remain an Eligible Employee
     for any reason (including death, disability or change in status) while his
     or her purchase right remains outstanding, then that purchase right shall
     immediately terminate, and all of the Participant's payroll deductions for
     the Purchase Interval in which the purchase right so terminates shall be
     immediately refunded. However, should the Participant cease to remain in
     active service by reason of an approved unpaid leave of absence, then the
     Participant shall have the right, exercisable up until the last business
     day of the Purchase Interval in which such leave commences, to (a) withdraw
     all the payroll deductions collected to date on his or her behalf for that
     Purchase Interval or (b) have such funds held for the purchase of shares on
     his or her behalf on the next scheduled Purchase Date. In no event,
     however, shall any further payroll deductions be collected on the
     Participant's behalf during such leave. Upon the Participant's return to
     active service (x) within ninety (90) days following the commencement of
     such leave or (y) prior to the expiration of any longer period for which
     such Participant's right

                                       5.
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     to reemployment with the Corporation is guaranteed by statute or contract,
     his or her payroll deductions under the Plan shall automatically resume at
     the rate in effect at the time the leave began, unless the Participant
     withdraws from the Plan prior to his or her return. An individual who
     returns to active employment following a leave of absence that exceeds in
     duration the applicable (x) or (y) time period will be treated as a new
     Employee for purposes of subsequent participation in the Plan and must
     accordingly re-enroll in the Plan (by making a timely filing of the
     prescribed enrollment forms) on or before the start date of any subsequent
     offering period in which he or she wishes to participate.

          G.   Change in Control.  Each outstanding purchase right shall
               -----------------
automatically be exercised, immediately prior to the effective date of any
Change in Control, by applying the payroll deductions of each Participant for
the Purchase Interval in which such Change in Control occurs to the purchase of
whole shares of Common Stock at a purchase price per share equal to eighty-five
percent (85%) of the lower of (i) the Fair Market Value per share of Common
Stock on the start date of the offering period in which such individual is
participating at the time of such Change in Control or (ii) the Fair Market
Value per share of Common Stock immediately prior to the effective date of such
Change in Control. However, the applicable limitation on the number of shares of
Common Stock purchasable per Participant shall continue to apply to any such
purchase, but not the limitation applicable to the maximum number of shares of
Common Stock purchasable in total by all Participants on any one Purchase Date.

          The Corporation shall use its best efforts to provide at least ten
(10) days' prior written notice of the occurrence of any Change in Control, and
Participants shall, following the receipt of such notice, have the right to
terminate their outstanding purchase rights prior to the effective date of the
Change in Control.

          H.   Proration of Purchase Rights.  Should the total number of shares
               ----------------------------
of Common Stock to be purchased pursuant to outstanding purchase rights on any
particular date exceed the number of shares then available for issuance under
the Plan, the Plan Administrator shall make a pro-rata allocation of the
available shares on a uniform and nondiscriminatory basis, and the payroll
deductions of each Participant, to the extent in excess of the aggregate
purchase price payable for the Common Stock pro-rated to such individual, shall
be refunded.

          I.   Assignability.  The purchase right shall be exercisable only by
               -------------
the Participant and shall not be assignable or transferable by the Participant.

          J.   Stockholder Rights.  A Participant shall have no stockholder
               ------------------
rights with respect to the shares subject to his or her outstanding purchase
right until the shares are purchased on the Participant's behalf in accordance
with the provisions of the Plan and the Participant has become a holder of
record of the purchased shares.

                                       6.
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     VIII. ACCRUAL LIMITATIONS

           A.   No Participant shall be entitled to accrue rights to acquire
Common Stock pursuant to any purchase right outstanding under this Plan if and
to the extent such accrual, when aggregated with (i) rights to purchase Common
Stock accrued under any other purchase right granted under this Plan and (ii)
similar rights accrued under other employee stock purchase plans (within the
meaning of Code Section 423)) of the Corporation or any Corporate Affiliate,
would otherwise permit such Participant to purchase more than Twenty-Five
Thousand Dollars ($25,000.00) worth of stock of the Corporation or any Corporate
Affiliate (determined on the basis of the Fair Market Value per share on the
date or dates such rights are granted) for each calendar year such rights are at
any time outstanding.

           B.   For purposes of applying such accrual limitations to the
purchase rights granted under the Plan, the following provisions shall be in
effect:

                (i)  The right to acquire Common Stock under each outstanding
     purchase right shall accrue in a series of installments on each successive
     Purchase Date during the offering period on which such right remains
     outstanding.

                (ii) No right to acquire Common Stock under any outstanding
     purchase right shall accrue to the extent the Participant has already
     accrued in the same calendar year the right to acquire Common Stock under
     one or more other purchase rights at a rate equal to Twenty-Five Thousand
     Dollars ($25,000.00) worth of Common Stock (determined on the basis of the
     Fair Market Value per share on the date or dates of grant) for each
     calendar year such rights were at any time outstanding.

          C.    If by reason of such accrual limitations, any purchase right of
a Participant does not accrue for a particular Purchase Interval, then the
payroll deductions that the Participant made during that Purchase Interval with
respect to such purchase right shall be promptly refunded.

           D.   In the event there is any conflict between the provisions of
this Article and one or more provisions of the Plan or any instrument issued
thereunder, the provisions of this Article shall be controlling.

     IX.   EFFECTIVE DATE AND TERM OF THE PLAN

           A.   The Plan was adopted by the Board on ___________, 1999, and
shall become effective at the Effective Time, provided no purchase rights
granted under the Plan shall be exercised, and no shares of Common Stock shall
be issued hereunder, until (i) the Plan shall have been approved by the
stockholders of the Corporation and (ii) the Corporation shall have complied
with all applicable requirements of the 1933 Act (including the registration of
the shares of Common Stock issuable under the Plan on a Form S-8 registration
statement filed with the Securities and Exchange Commission), all applicable
listing requirements of any stock

                                       7.
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exchange (or the Nasdaq National Market, if applicable) on which the Common
Stock is listed for trading and all other applicable requirements established by
law or regulation. In the event such stockholder approval is not obtained, or
such compliance is not effected, within twelve (12) months after the date on
which the Plan is adopted by the Board, the Plan shall terminate and have no
further force or effect, and all sums collected from Participants during the
initial offering period hereunder shall be refunded.

          B.   Unless sooner terminated by the Board, the Plan shall terminate
upon the earliest of (i) the last business day in January 2010, (ii) the date on
which all shares available for issuance under the Plan shall have been sold
pursuant to purchase rights exercised under the Plan or (iii) the date on which
all purchase rights are exercised in connection with a Change in Control. No
further purchase rights shall be granted or exercised, and no further payroll
deductions shall be collected, under the Plan following such termination.

     X.   AMENDMENT OF THE PLAN

          A.   The Board may alter, amend, suspend or terminate the Plan at any
time to become effective immediately following the close of any Purchase
Interval. However, the Plan may be amended or terminated immediately upon Board
action, if and to the extent necessary to assure that the Corporation will not
recognize, for financial reporting purposes, any compensation expense in
connection with the shares of Common Stock offered for purchase under the Plan,
should the financial accounting rules applicable to the Plan at the Effective
Time be subsequently revised so as to require the Corporation to recognize
compensation expense in the absence of such amendment or termination.

          B.   In no event may the Board effect any of the following amendments
or revisions to the Plan without the approval of the Corporation's stockholders:
(i) increase the number of shares of Common Stock issuable under the Plan,
except for permissible adjustments in the event of certain changes in the
Corporation's capitalization, (ii) alter the purchase price formula so as to
reduce the purchase price payable for the shares of Common Stock purchasable
under the Plan or (iii) modify the eligibility requirements for participation in
the Plan.

     XI.  GENERAL PROVISIONS

          A.   All costs and expenses incurred in the administration of the Plan
shall be paid by the Corporation; however, each Plan Participant shall bear all
costs and expenses incurred by such individual in the sale or other disposition
of any shares purchased under the Plan.

          B.   Nothing in the Plan shall confer upon the Participant any right
to continue in the employ of the Corporation or any Corporate Affiliate for any
period of specific duration or interfere with or otherwise restrict in any way
the rights of the Corporation (or any Corporate Affiliate employing such person)
or of the Participant, which rights are hereby expressly reserved by each, to
terminate such person's employment at any time for any reason, with or without
cause.

                                       8.
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          C.   The provisions of the Plan shall be governed by the laws of the
State of California without resort to that State's conflict-of-laws rules.

                                       9.
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                                  Schedule A


                         Corporations Participating in
                         Employee Stock Purchase Plan
                           As of the Effective Time
                           ------------------------

                                Sequenom, Inc.
<PAGE>

                                    APPENDIX
                                    --------
          The following definitions shall be in effect under the Plan:

          A.   Base Salary shall mean the regular base salary paid to a
               -----------
Participant by one or more Participating Companies during such individual's
period of participation in one or more offering periods under the Plan and shall
be calculated before deduction of (A) any income or employment tax withholdings
or (B) any contributions made by the Participant to any Code Section 401(k)
salary deferral plan or any Code Section 125 cafeteria benefit program now or
hereafter established by the Corporation or any Corporate Affiliate. Base Salary
shall not include (i) any overtime payments, bonuses, commissions, profit-
sharing distributions or other incentive-type payments or (ii) any contributions
made by the Corporation or any Corporate Affiliate on the Participant's behalf
to any employee benefit or welfare plan now or hereafter established (other than
Code Section 401(k) or Code Section 125 contributions deducted from such Base
Salary).

          B.   Board shall mean the Corporation's Board of Directors.
               -----

          C.   Change in Control shall mean a change in ownership of the
               -----------------
Corporation pursuant to any of the following transactions:

               (i)    a merger or consolidation in which securities possessing
     more than fifty percent (50%) of the total combined voting power of the
     Corporation's outstanding securities are transferred to a person or persons
     different from the persons holding those securities immediately prior to
     such transaction, or

               (ii)   the sale, transfer or other disposition of all or
     substantially all of the assets of the Corporation in complete liquidation
     or dissolution of the Corporation, or

               (iii)  the acquisition, directly or indirectly, by a person or
     related group of persons (other than the Corporation or a person that
     directly or indirectly controls, is controlled by or is under common
     control with the Corporation) of beneficial ownership (within the meaning
     of Rule 13d-3 of the 1934 Act) of securities possessing more than fifty
     percent (50%) of the total combined voting power of the Corporation's
     outstanding securities pursuant to a tender or exchange offer made directly
     to the Corporation's stockholders.

          D.   Code shall mean the Internal Revenue Code of 1986, as amended.
               ----

          E.   Common Stock shall mean the Corporation's common stock.
               ------------

                                      A-1
<PAGE>

          F.   Corporate Affiliate shall mean any parent or subsidiary
               -------------------
corporation of the Corporation (as determined in accordance with Code
Section 424), whether now existing or subsequently established.

          G.   Corporation shall mean Sequenom, Inc., a Delaware corporation,
               -----------
and any corporate successor to all or substantially all of the assets or voting
stock of Sequenom, Inc. that shall by appropriate action adopt the Plan.

          H.   Effective Time shall mean the time at which the Underwriting
               --------------
Agreement is executed and the Common Stock priced for the initial public
offering of such Common Stock. Any Corporate Affiliate that becomes a
Participating Corporation after such Effective Time shall designate a subsequent
Effective Time with respect to its employee-Participants.

          I.   Eligible Employee shall mean any person who is employed by a
               -----------------
Participating Corporation on a basis under which he or she is regularly expected
to render more than twenty (20) hours of service per week for more than five (5)
months per calendar year for earnings considered wages under Code
Section 3401 (a).

          J.   Fair Market Value per share of Common Stock on any relevant date
               -----------------
shall be determined in accordance with the following provisions:

               (i)   If the Common Stock is at the time traded on the Nasdaq
     National Market, then the Fair Market Value shall be the closing selling
     price per share of Common Stock on the date in question, as such price is
     reported by the National Association of Securities Dealers on the Nasdaq
     National Market. If there is no closing selling price for the Common Stock
     on the date in question, then the Fair Market Value shall be the closing
     selling price on the last preceding date for which such quotation exists.

               (ii)  If the Common Stock is at the time listed on any Stock
     Exchange, then the Fair Market Value shall be the closing selling price per
     share of Common Stock on the date in question on the Stock Exchange
     determined by the Plan Administrator to be the primary market for the
     Common Stock, as such price is officially quoted in the composite tape of
     transactions on such exchange. If there is no closing selling price for the
     Common Stock on the date in question, then the Fair Market Value shall be
     the closing selling price on the last preceding date for which such
     quotation exists.

               (iii)  For purposes of the initial offering period that begins at
     the Effective Time, the Fair Market Value shall be deemed to be equal to
     the price per share at which the Common Stock is sold in the initial public
     offering pursuant to the Underwriting Agreement.

          K.   1933 Act shall mean the Securities Act of 1933, as amended.
               --------

                                      A-2
<PAGE>

          L.   Participant shall mean any Eligible Employee of a Participating
               -----------
Corporation who is actively participating in the Plan.

          M.   Participating Corporation shall mean the Corporation and such
               -------------------------
Corporate Affiliate or Affiliates as may be authorized from time to time by the
Board to extend the benefits of the Plan to their Eligible Employees.  The
Participating Corporations in the Plan are listed in attached Schedule A.

          N.   Plan shall mean the Corporation's 1999 Employee Stock Purchase
               ----
Plan, as set forth in this document.

          O.   Plan Administrator shall mean the committee of two (2) or more
               ------------------
Board members appointed by the Board to administer the Plan.

          P.   Purchase Date shall mean the last business day of each Purchase
               -------------
Interval.  The initial Purchase Date shall be July 31, 2000.

          Q.   Purchase Interval shall mean each successive six (6)-month period
               -----------------
within a particular offering period at the end of which there shall be purchased
shares of Common Stock on behalf of each Participant.

          R.   Stock Exchange shall mean either the American Stock Exchange or
               --------------
the New York Stock Exchange.

          S.   Underwriting Agreement shall mean the agreement between the
               ----------------------
Corporation and the underwriter or underwriters managing the initial public
offering of the Common Stock.

                                      A-3