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Exhibit 10.50

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AMENDED AND RESTATED 1996

NONEMPLOYEE DIRECTORS STOCK OPTION PLAN OF

AFFYMETRIX, INC.

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TABLE OF CONTENTS

 
   
  Page

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1.
 
PURPOSES OF THE PLAN
 
3
2.
 
DEFINITIONS
 
3
3.
 
ELIGIBLE PERSONS
 
4
4.
 
STOCK SUBJECT TO THIS PLAN
 
4
5
 
ADMINISTRATION
 
4
6.
 
GRANT OF OPTIONS
 
4
7.
 
TERMS AND CONDITIONS OF OPTIONS
 
5
8.
 
MANNER OF EXERCISE
 
7
9.
 
NO RIGHT TO DIRECTORSHIP
 
7
10.
 
LEGAL REQUIREMENTS
 
7
11.
 
AMENDMENTS TO PLAN
 
7
12.
 
ADOPTION; SHAREHOLDER APPROVAL; TERM
 
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AMENDED AND RESTATED 1996
NONEMPLOYEE DIRECTORS STOCK OPTION PLAN OF
AFFYMETRIX, INC.

1.  PURPOSES OF THE PLAN

    The purposes of the 1996 Nonemployee Directors Stock Option Plan of
Affymetrix, Inc. a Delaware corporation, are to:

(a)Encourage Nonemployee Directors to improve operations and increase profits of
the Company;

(b)Encourage Nonemployee Directors to accept or continue their association with
the Company; and

(c)Increase the interest of Nonemployee Directors in the Company's welfare
through participation in the growth in value of the Common Stock of the Company.

    Options granted hereunder shall be "Nonstatutory Options", and shall not
include "incentive stock options" intended to satisfy the requirements of
Section 422 of the Internal Revenue Code of 1986, as amended.

2.  DEFINITIONS

    As used herein, the following definitions shall apply:

    (a)  "Administrator"  shall mean the entity, either the Board or the
Committee, responsible for administering this Plan, as provided in Section 3.

    (b)  "Board"  shall mean the Board of Directors of the Company, as
constituted from time to time.

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

    (d)  "Committee"  shall mean the committee, if any, appointed by the Board
in accordance with Section 5(a) to administer this Plan.

    (e)  "Common Stock"  shall mean the Common Stock of the Company.

    (f)  "Company"  shall mean Affymetrix, Inc., a Delaware corporation.

    (g)  "Fair Market Value"  shall mean, as of the date in question, the last
transaction price quoted by the Nasdaq National Market System on the date of
grant; provided, however, that if the Common Stock is not traded on such market
system or the foregoing shall otherwise be in appropriate, then the Fair Market
Value shall be determined by the Administrator in good faith at its sole
discretion and on such basis as it shall deem appropriate. Such determination
shall be conclusive and binding on all persons.

    (h)  "Nonemployee Director"  shall mean any person who is a member of the
Board but is not an employee of the Company and has not been an employee of the
Company or any Subsidiary of the Company at any time during the preceding
12 months. Service as a director does not in itself constitute employment for
purposes of this definition.

    (i)  "Option"  shall mean a stock option granted pursuant to this Plan. Each
Option shall be a nonstatutory option not intended to qualify as an incentive
stock option within the meaning of Section 422 of the Code.

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    (j)  "Option Agreement"  shall mean the written agreement described in
Section 6.4 evidencing the grant of an Option to a Nonemployee Director and
containing the terms, conditions and restrictions pertaining to such Option.

    (k)  "Option Shares"  shall mean the Shares subject to an Option granted
under this Plan.

    (1)  "Optionee"  shall mean a Nonemployee Director who holds an Option.

    (m)  "Plan"  shall mean this Amended and Restated 1996 Nonemployee Directors
Stock Option Plan of Affymetrix, Inc., as it may be amended from time to time.

    (n)  "Section"  unless the context clearly indicates otherwise, shall refer
to a Section of this Plan.

    (o)  "Share"  shall mean a share of Common Stock, as adjusted in accordance
with Section 7.1.

    (p)  "Subsidiary"  shall mean a "subsidiary corporation" of the Company,
whether now or hereafter existing, within the meaning of Section 424(f) of the
Code, but only for so long as it is a "subsidiary corporation".

3.  ELIGIBLE PERSONS

    Every person who at the date of grant of an Option is a Nonemployee Director
is eligible to receive Options under this Plan, except that a Nonemployee
Director who is elected to the Board on or after July 8, 1999, shall not be
eligible for any grants of Options if he or she is affiliated with a holder of
10% or more of the voting power of the Company's capital stock.

4.  STOCK SUBJECT TO THIS PLAN

    Subject to Section 7.1 of this Plan, the maximum aggregate number of Shares
which may be issued on exercise of Options granted pursuant to this Plan is
600,000 Shares (as adjusted to reflect the Company's 2-for-1 stock split on
August 21, 2000). The Shares covered by the portion of any grant under the Plan
which expires unexercised shall become available again for grants under the
Plan.

5.  ADMINISTRATION

    5.1  Administrator.  This Plan shall be administered by the Board, or by a
committee (the "Committee") of at least two Board members to which
administration of the Plan is delegated (in either case, the "Administrator").

    5.2  Authority.  Subject to the other provisions of this Plan, the
Administrator shall have the authority, in its sole discretion: (i) to determine
the Fair Market Value of the Shares subject to options; (ii) to interpret this
Plan; (iii) to prescribe, amend and rescind rules and regulations relating to
this Plan; (iv) to defer (with the consent of the Optionee) or accelerate the
exercise date of any Option; (v) to authorize any person to execute on behalf of
the Company any instrument evidencing the grant of an Option; and (vi) to make
all other determinations deemed necessary or advisable for the administration of
this Plan. The Administrator may delegate nondiscretionary administrative duties
to such employees of the Company as it deems proper.

    5.3  Final and Binding.  All questions of interpretation, implementation and
application of this Plan shall be determined by the Administrator. Such
determination shall be final and binding on all persons.

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6.  GRANT OF OPTIONS

    6.  Directors Now in Office.  Those Nonemployee Directors in office on the
date this Plan was approved by the Board received a grant of options in
December 1995. Subject to the terms and conditions of this Plan, on the date of
the first meeting of the Board immediately after each annual meeting of
shareholders of the Company that occurs on or after January 1, 2001 (even if
held on the same day as the meeting of shareholders), the Company shall grant to
each such Nonemployee Director then in office an option to purchase 10,000
Shares at an exercise price equal to the Fair Market Value of such Shares on the
date of such option grant.

    6.2  Initial Grants to Future Directors.  Subject to the terms and
conditions of this Plan, if any person who is not an officer or employee of the
Company is first elected or appointed as a member of the Board on or after the
date of adoption of this Plan by the Board, then on the effective date of such
appointment or election of such person, the Company shall grant to such
Nonemployee Director an Option to purchase 20,000 Shares at an exercise price
equal to the Fair Market Value of such Shares on the date of such option grant.

    6.3  Annual Grants to Future Directors.  Subject to the terms and conditions
of this Plan, on the date of the first meeting of the Board immediately
following each annual meeting of shareholders of the Company (even if held on
the same day as the meeting of shareholders) which is held at least 54 months
after the date of the initial option grant to a Nonemployee Director identified
in Section 6.2 above, and thereafter, the Company shall grant to each such
Nonemployee Director than in office an Option to purchase 10,000 Shares at an
exercise price equal to the Fair Market Value of such Shares on the date of such
option grant.

    6.4  Option Agreements.  No Options shall be granted under this Plan after
10 years after the date of adoption of this Plan by the Board. Each Option shall
be evidenced by a written Option Agreement, in form satisfactory to the Company,
executed by the Company and the Nonemployee Director to whom such Option is
granted; provided, however, that the failure by the Company, the Nonemployee
Director or both to execute such an agreement shall not invalidate the granting
of an Option.

7.  TERMS AND CONDITIONS OF OPTIONS

    Each Option granted under this Plan shall be subject to the terms and
conditions set forth in this Section 7.

    7.1  Changes in Capital Structure.  Subject to Section 7.2, if the Common
Stock is changed by reason of a stock split, reverse stock split, stock dividend
or re-capitalization, or converted into or exchanged for other securities as a
result of a merger, consolidation or reorganization, appropriate adjustments
shall be made in: (a) the number and class of shares of Common Stock subject to
this Plan and each Option outstanding under this Plan; and (b) the exercise
price of each outstanding Option; provided, however, that the Company shall not
be required to issue fractional shares as a result of any such adjustments. Each
such adjustment shall be subject to approval by the Administrator in its sole
discretion.

    7.2  Corporate Transactions.  In connection with an acquisition of the
Company affected by a merger, consolidation, sale of all or substantially all of
the Company's assets, acquisition of shares, or any like occurrence in which the
Company is involved, the Company's right of repurchase set forth in Section 7.3
shall expire with respect to twice the number of Options otherwise determined
pursuant to Section 7.3. The Administrator shall have the authority, in its sole
discretion to determine the time prior to consummation of such acquisition when
such increased expiration of the right to repurchase shall become effective.

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    7.3  Time of Option Exercise; Repurchase Right.  Subject to the other
provisions of this Plan, each option granted pursuant to this Plan shall be for
a term of 10 years and two days. Each Option granted pursuant to this Plan shall
be exercisable in full six months after the date of grant. The Company shall
have a right of repurchase at the Option exercise price (i) with respect to
Shares purchased upon exercise of Options granted pursuant to Section 6.2 which
shall expire with respect to 50% of the number of Shares covered by the Option
grant on each of the first two anniversaries of the date of grant and (ii) with
respect to Shares purchased upon exercise of Options granted pursuant to
Sections 6.1 and 6.3 which shall expire with respect to 100% of the number of
Shares covered by the Option grant on the first anniversary of the date of
grant. The Company may exercise its repurchase right by written notice to the
Director within 120 days after the date such Director ceases to act as a
Director of the Company.

    7.4  Limitation on Other Grants.  The Administrator shall have no discretion
to grant Options under this Plan other than as set forth in Sections 6.1, 6.2
and 6.3.

    7.5  Nonassignability of Option Rights.  No Option granted under this Plan
shall be assignable or otherwise transferable by the Optionee, except by will or
the laws of descent and distribution, or pursuant to a qualified domestic
relations order as defined by the Code. During the life of an Optionee, an
Option shall be exercisable only by the Optionee.

    7.6  Payment.  Except as provided below, payment in full, in cash, shall be
made for all Option Shares purchased at the time written notice of exercise of
an Option is given to the Company, and proceeds of any payment shall constitute
general funds of the Company. At the time an Option is granted or exercised, the
Administrator, in the exercise of its absolute discretion, may authorize any one
or more of the following additional methods of payment: (a) acceptance of the
Optionee's full recourse promissory note for all or part of the Option price,
less any par value per share, which must be paid in cash, payable on such terms
and bearing such interest rate as determined by the Administrator (but in no
event less than the minimum interest rate specified under the Code at which no
additional interest on debt instruments of such type would be imputed), which
promissory note may be either secured or unsecured in such manner as the
Administrator shall approve (including, without limitation, by a security
interest in the Shares); (b) delivery by the optionee of Common Stock already
owned by the optionee for all or part of the option price, provided the Fair
Market Value of such Common Stock is equal on the date of exercise to the Option
price; provided, however, that if an Optionee has exercised any portion of any
Option granted by the Company by delivery of Common Stock, the Optionee may not,
within six months following such exercise, exercise any Option granted under
this Plan by delivery of Common Stock; and (c) any other consideration and
method of payment to the extent permitted under the California Corporations
Code.

    7.7  Termination as Director.  Unless determined otherwise by the
Administrator in its absolute discretion, to the extent not already expired or
exercised, an Option shall terminate at the earlier of: (a) the expiration of
the term of the Option; or (b) three months after the last day served by the
optionee as a director of the Company; provided, that an Option shall be
exercisable after the date of termination of service as a director only to the
extent exercisable on the date of termination; and provided further, that if
termination of service as a director is due to the Optionee's death or
"disability" (as determined in accordance with Section 22(e)(3) of the Code),
the Optionee, or the Optionee's personal representative (or any other person who
acquires the Option from the Optionee by will or the applicable laws of descent
and distribution), may at any time within 18 months after the termination of
service as a director (or such lesser period as is specified in the Option
Agreement but in no event after the expiration of the term of the Option),
exercise the rights to the extent they were exercisable on the date of the
termination.

    7.8  Withholding and Employment Taxes.  At the time of exercise of an Option
(or at such later time(s) as the Company may prescribe), the Optionee shall
remit to the Company in cash all applicable

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federal and state withholding and employment taxes. If authorized by the
Administrator in its sole discretion, an Optionee shall be permitted to elect,
by means of a form of election to be prescribed by the Administrator, to have
shares of Common Stock- which are acquired upon exercise of the Option withheld
by the Company or to tender to the Company other shares of Common Stock or other
securities of the Company owned by the Optionee on the date of determination of
the amount of tax to be withheld as a result of the exercise of such Option (the
"Tax Date") to pay the amount of tax that is required by law to be withheld by
the Company as a result of the exercise of such option. Any securities so
withheld or tendered shall be valued by the Company as of the Tax Date.

    7.9  Option Term.  Each Option granted hereunder shall expire 10 years and
two days after the date of the grant.

8.  MANNER OF EXERCISE

    8.  Notice.  An Optionee wishing to exercise an Option shall give written
notice to the Company at its principal executive office, to the attention of the
officer of the Company designated by the Administrator, accompanied by payment
of the exercise price as provided in Section 7.6 and, if required, by payment of
any federal or state withholding or employment taxes required to be withheld by
virtue of exercise of the Option. The date the Company receives written notice
of an exercise hereunder accompanied by payment of the exercise price and any
required federal or state withholding or employment taxes will be considered as
the date such Option was exercised. Unless otherwise provided by the
Administrator, Options may be exercised only twice in any calendar year.

    8.2  Stock Issuance.  Promptly after the date an option is exercised, the
Company shall, without stock issue or transfer taxes to the optionee or other
person entitled to exercise the option, deliver to the Optionee or such other
person a certificate or certificates for the requisite number of shares of
Common Stock. An Optionee or transferee of an Optionee shall not have any
privileges as a stockholder with respect to any Common Stock covered by the
Option until the date of issuance of a stock certificate.

9.  NO RIGHT TO DIRECTORSHIP

    Neither this Plan nor any Option granted hereunder shall confer upon any
optionee any right with respect to continuation of the Optionee's membership on
the Board or shall interfere in any way with provisions in the Company's
Articles of Incorporation and By-Laws relating to the election, appointment,
terms of office, and removal of members of the Board.

10. LEGAL REQUIREMENTS

    The Company shall not be obligated to offer or sell any Shares upon exercise
of any option except in compliance with all applicable securities laws and the
regulations of any stock exchange on which the Company's securities may then be
listed. Certificates evidencing Shares acquired upon exercise of Options shall
bear any legend required by, or useful for purposes of compliance with,
applicable securities laws, this Plan or the Option Agreements.

11. AMENDMENTS TO PLAN

    The Board may amend this Plan at any time. Without the consent of an
optionee, no amendment may adversely affect outstanding Options. No amendment
shall require shareholder approval unless:

(a)shareholder approval is required by applicable laws, regulations or rules; or

(b)the Board otherwise concludes that shareholder approval is advisable.

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12. ADOPTION; SHAREHOLDER APPROVAL; TERM

    This Plan was adopted by the Board of Directors on March 27, 1996 and
approved by the shareholders on April 15, 1996. The Plan was amended by the
Board of Directors on September 30, 1996, amended by the Board of Directors on
July 8, 1999 and amended and restated by the Board of Directors on April 25,
2001. This Plan shall terminate on March 27, 2006, unless terminated earlier by
the Board. The Board may terminate this Plan at any time without shareholder
approval. No Options shall be granted after termination of this Plan, but
termination shall not affect rights and obligations under then outstanding
options.

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TABLE OF CONTENTS
AMENDED AND RESTATED 1996 NONEMPLOYEE DIRECTORS STOCK OPTION PLAN OF AFFYMETRIX, INC.