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                                                                    EXHIBIT 4.3

                               Up to $225,000,000

                                Affymetrix, Inc.

                 4.75% Convertible Subordinated Notes due 2007

                         REGISTRATION RIGHTS AGREEMENT


                                                               February 14, 2000

Credit Suisse First Boston Corporation,
as Representative of the several Initial
Purchasers referred to herein,
c/o Credit Suisse First Boston Corporation
Eleven Madison Avenue
New York, New York  10010-3629

Dear Sirs:

     Affymetrix, Inc., a Delaware corporation (the "Company"), proposes to issue
and sell to Credit Suisse First Boston Corporation ("CSFBC") and the other
initial purchasers named in Schedule A to the Purchase Agreement (as defined
below) (collectively, the "Initial Purchasers"), upon the terms set forth in a
purchase agreement dated as of February 8, 2000 (the "Purchase Agreement")
between the Company and the Initial Purchasers, $175,000,000 aggregate principal
amount (plus up to an additional $50,000,000 principal amount) of 4.75%
Convertible Subordinated Notes Due 2007 (the "Notes") of the Company. The Notes
will be convertible into shares of Common Stock, par value $0.01 per share, of
the Company (the "Common Stock") at the conversion price set forth in the
Offering Circular dated February 8, 2000. The Notes will be issued pursuant to
an Indenture, dated as of February 14, 2000 (the "Indenture"), between the
Company and The Bank of New York (the "Trustee"). As an inducement to the
Initial Purchasers to enter into the Purchase Agreement and in satisfaction of a
condition to the Initial Purchasers' obligations thereunder, the Company agrees
with the Initial Purchasers, (i) for the benefit of the Initial Purchasers and
(ii) for the benefit of the holders of the Notes and the Common Stock issuable
upon conversion of the Notes (collectively, the "Securities") from time to time
until such time as such Securities have been sold pursuant to a Shelf
Registration Statement (as defined below) (each of the foregoing a "Holder" and
together the "Holders"), as follows:

     1. SHELF REGISTRATION. The Company shall take the following actions:

     (a) The Company shall, at its cost, prepare and, as promptly as practicable
(but in no event more than 90 days after so required or requested pursuant to
this Section 1) file with the Securities and Exchange Commission (the
"Commission")

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and thereafter shall use its commercially reasonable best efforts to cause to be
declared effective as soon as practicable a registration statement on Form S-3
(the "Shelf Registration Statement") covering the offer and sale of the Transfer
Restricted Securities (as defined in Section 5 hereof) by the Holders thereof
from time to time in accordance with the methods of distribution set forth in
the Shelf Registration Statement and Rule 415 under the Securities Act of 1933,
as amended (the "Securities Act") (hereinafter, the "Shelf Registration");
PROVIDED, HOWEVER, that no Holder (other than the Initial Purchasers) shall be
entitled to have the Securities held by it covered by such Shelf Registration
Statement unless such Holder agrees in writing to be bound by all the provisions
of this Agreement applicable to such Holder.

     (b) The Company shall use its commercially reasonable best efforts to keep
the Shelf Registration Statement continuously effective in order to permit the
prospectus included therein (the "Prospectus") to be lawfully delivered by the
Holders of the relevant Securities, for a period of two years (or for such
longer period if extended pursuant to Section 2(h) below) from the date of its
effectiveness or such shorter period that will terminate when all the Securities
covered by the Shelf Registration Statement (i) have been sold pursuant thereto
or (ii) may be sold pursuant to Rule 144(k) under the Securities Act (or any
successor rule therefore), assuming for this purpose that the Holders thereof
are not affiliates of the Company (in any such case, such period being called
the "Shelf Registration Period"). The Company shall be deemed not to have used
its commercially reasonable best efforts to keep the Shelf Registration
Statement effective during the requisite period if it voluntarily takes any
action that would result in Holders of Securities covered thereby not being able
to offer and sell such Securities during that period, unless such action is (i)
required by applicable law or (ii) taken by the Company in good faith and for
valid business reasons upon the occurrence of any event contemplated by Section
2(b)(v) below, and the Company thereafter complies with the requirements of
Section 2(h).

     (c) Notwithstanding any other provisions of this Agreement to the contrary,
the Company shall cause the Shelf Registration Statement and the Prospectus and
any amendment or supplement thereto, as of the effective date of the Shelf
Registration Statement, amendment or supplement, (i) to comply in all material
respects with the applicable requirements of the Securities Act and the rules
and regulations of the Commission and (ii) not to contain any untrue statement
of a material fact or omit to state a material fact required to be stated
therein or necessary to make the statements therein, in light of the
circumstances under which they were made, not misleading.

     2. REGISTRATION PROCEDURES. In connection with the Shelf Registration
contemplated by Section 1 hereof, the following provisions shall apply:

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     (a) The Company shall (i) furnish to each of the Initial Purchasers, prior
to the filing thereof with the Commission, a copy of the Shelf Registration
Statement and each amendment thereof and each amendment or supplement, if any,
to the prospectus included therein and, in the event that an Initial Purchaser
(with respect to any portion of an unsold allotment from the original offering)
is participating in the Shelf Registration Statement, use its commercially
reasonable best efforts to reflect in each such document, when so filed with the
Commission, such comments as such Initial Purchaser reasonably may propose and
(ii) include the names of the Holders who propose to sell Securities pursuant to
the Shelf Registration Statement, as selling security holders.

     (b) The Company shall give written notice to the Initial Purchasers and the
Holders (which notice pursuant to clauses (ii)-(v) hereof shall be accompanied
by an instruction to suspend the use of the prospectus until the requisite
changes have been made):

          (i) when the Shelf Registration Statement or any amendment thereto has
     been filed with the Commission and when the Shelf Registration Statement or
     any post-effective amendment thereto has become effective;

         (ii) of any request by the Commission for amendments or supplements to
     the Shelf Registration Statement or the prospectus included therein or for
     additional information;

        (iii) of the issuance by the Commission of any stop order suspending
     the effectiveness of the Shelf Registration Statement or the initiation of
     any proceedings for that purpose;

         (iv) of the receipt by the Company or its legal counsel of any
     notification with respect to the suspension of the qualification of the
     Securities for sale in any jurisdiction or the initiation or threatening of
     any proceeding for such purpose; and

          (v) of the happening of any event or circumstance that would require
     the Company to make changes in the Shelf Registration Statement or the
     Prospectus in order that the Shelf Registration Statement or the Prospectus
     does not contain an untrue statement of a material fact nor omit to state a
     material fact required to be stated therein or necessary to make the
     statements therein (in the case of the Prospectus, in light of the
     circumstances under which they were made) not misleading, which written
     notice need not provide any detail


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          as to the nature of such event.

     (c) The Company shall make every reasonable effort to obtain the
withdrawal, at the earliest possible time, of any order suspending the
effectiveness of the Shelf Registration Statement.

     (d) The Company shall furnish to each Holder of Securities included within
the coverage of the Shelf Registration, without charge, at least one copy of the
Shelf Registration Statement and any post-effective amendment thereto, including
financial statements and schedules, and, if the Holder so requests in writing,
all exhibits thereto (including those, if any, incorporated by reference).

     (e) The Company shall, during the Shelf Registration Period, deliver to
each Holder of Securities included within the coverage of the Shelf Registration
Statement, without charge, as many copies of the Prospectus (including each
preliminary prospectus) included in the Shelf Registration Statement and any
amendment or supplement thereto as such person may reasonably request. The
Company consents, subject to the provisions of this Agreement, to the use of the
Prospectus or any amendment or supplement thereto by each of the selling Holders
in connection with the offering and sale of the Securities covered by the
Prospectus, or any amendment or supplement thereto, included in the Shelf
Registration Statement.

     (f) Prior to any public offering of the Securities pursuant to the Shelf
Registration Statement, the Company shall register or qualify or cooperate with
the Holders of the Securities included therein and their respective counsel in
connection with the registration or qualification of such Securities for offer
and sale under the securities or "blue sky" laws of such states of the United
States as any such Holder reasonably requests in writing and do any and all
other acts or things necessary or advisable to enable the offer and sale in such
jurisdictions of the Securities covered by the Shelf Registration Statement;
PROVIDED, HOWEVER, that the Company shall not be required to (i) qualify
generally to do business in any jurisdiction where it is not then so qualified
or (ii) take any action which would subject it to general service of process or
to taxation in any jurisdiction where it is not then so subject.

     (g) The Company shall cooperate with the Holders of the Securities to
facilitate the timely preparation and delivery of certificates representing the
Securities to be sold pursuant to the Shelf Registration Statement free of any
restrictive legends and in such denominations and registered in such names as
the Holders may request a reasonable period of time prior to sales of the
Securities pursuant to the Shelf


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Registration Statement.

     (h) Upon the occurrence of any event contemplated by paragraphs (ii)
through (v) of Section 2(b) above during the period for which the Company is
required to maintain an effective Shelf Registration Statement, the Company
shall, as required hereby, prepare and file a post-effective amendment to the
Shelf Registration Statement or an amendment or supplement to the Prospectus and
any other required document so that, as thereafter delivered to Holders or
purchasers of Securities, the Prospectus will not contain an untrue statement of
a material fact or omit to state any material fact required to be stated therein
or necessary to make the statements therein, in light of the circumstances under
which they were made, not misleading. If the Company notifies the Initial
Purchasers and the Holders in accordance with paragraphs (ii) through (v) of
Section 2(b) above to suspend the use of the Prospectus until the requisite
changes to the Prospectus have been made, then the Initial Purchasers and the
Holders shall suspend use of such prospectus and the period of effectiveness of
the Shelf Registration Statement provided for in Section 1(b) above shall be
extended by the number of days from and including the date of giving such notice
to and including the date when the Initial Purchasers and the Holders shall have
received such amended or supplemented prospectus pursuant to this Section 2(h).
Any such amendment, supplement or document will be prepared and filed as
promptly as practicable under the circumstances, as determined in good faith by
the Company, it being understood that the Company may have bona fide reasons to
delay such preparation and filing for a period which may not in any event exceed
60 days.

     (i) Not later than the effective date of the Shelf Registration Statement,
the Company will provide CUSIP numbers for the Notes and the Common Stock
registered under the Shelf Registration Statement, and provide the Trustee with
printed certificates for such Notes, in a form eligible for deposit with The
Depository Trust Company.

     (j) The Company will comply with all rules and regulations of the
Commission to the extent and so long as they are applicable to the Shelf
Registration and will make generally available to its security holders (or
otherwise provide in accordance with Section 11(a) of the Securities Act) an
earnings statement satisfying the provisions of Section 11(a) of the Securities
Act, no later than 45 days after the end of a 12-month period (or 90 days, if
such period is a fiscal year) beginning with the first month of the Company's
first fiscal quarter commencing after the effective date of the Shelf
Registration Statement, which statement shall cover such 12-month period.

     (k) The Company shall cause the Indenture to be qualified under the Trust
Indenture Act of 1939, as amended (the "Trust Indenture Act"), in a timely
manner and containing such changes, if any, as shall be necessary for such
qualification. In the

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event that such qualification would require the appointment of a new trustee
under the Indenture, the Company shall appoint a new trustee thereunder pursuant
to the applicable provisions of the Indenture.

     (l) The Company may require each Holder of Securities to be sold pursuant
to the Shelf Registration Statement to furnish to the Company such information
regarding the Holder and the distribution of the Securities as the Company may
from time to time reasonably require for inclusion in the Shelf Registration
Statement, and the Company may exclude from such registration the Securities of
any Holder that fails to furnish such information within a reasonable time after
receiving such request.

     (m) The Company shall enter into such customary agreements (including, if
requested, an underwriting agreement in customary form) and take all other
actions, if any, as any Holder shall reasonably request in order to facilitate
the disposition of the Securities pursuant to the Shelf Registration, PROVIDED,
HOWEVER, that the Company shall not be required to facilitate an underwritten
offering pursuant to the Shelf Registration Statement by any Holders unless the
offering relates to at least $50,000,000 principal amount of the Notes or the
equivalent number of shares of Common Stock into which such Notes are
convertible.

     (n) The Company shall (i) make reasonably available for inspection by the
Holders, any underwriter participating in any distribution pursuant to the Shelf
Registration Statement and any attorney, accountant or other agent retained by
the Holders or any such underwriter, all relevant financial and other records,
pertinent corporate documents and properties of the Company and (ii) cause the
Company's officers, directors, employees, accountants and auditors to supply all
relevant information reasonably requested by the Holders or any such
underwriter, attorney, accountant or agent in connection with the Shelf
Registration Statement, in each case, as shall be reasonably necessary to enable
such persons to conduct a reasonable investigation within the meaning of Section
11 of the Securities Act; PROVIDED, HOWEVER, that the foregoing inspection and
information gathering (i) shall be coordinated on behalf of the Initial
Purchasers by you and on behalf of the other parties, by one counsel designated
by and on behalf of the other parties as described in Section 3 hereof.

     (o) The Company, if requested by any Holder of Securities covered by Shelf
Registration Statement, shall cause (i) its counsel (which may include the
Company's general counsel for one or more of the opinions) to deliver an opinion
and updates thereof relating to the Securities in customary form addressed to
such Holders and the managing underwriters, if any, thereof, and dated, in the
case of the initial opinion, the effective date of the Shelf Registration
Statement (it being agreed that the

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matters to be covered by such opinion shall include, without limitation, (A) the
due incorporation and good standing of the Company; (B) the qualification of the
Company to transact business as a foreign corporation; the due authorization,
execution and delivery of the relevant agreement of the type referred to in
Section 2(m) hereof; (C) the due authorization, execution, authentication and
issuance, and the validity and enforceability, of the Securities; (D) the
absence of material legal or governmental proceedings involving the Company; (E)
the absence of governmental approvals required to be obtained in connection with
the Shelf Registration Statement, the offering and sale of the Securities, or
any agreement of the type referred to in Section 2(m) hereof; (F) the compliance
as to form of the Shelf Registration Statement and any documents incorporated by
reference therein and of the Indenture with the requirements of the Securities
Act and the Trust Indenture Act, respectively; and, (G) as of the date of the
opinion and as of the effective date of the Shelf Registration Statement or most
recent post-effective amendment thereto, as the case may be, the absence from
the Shelf Registration Statement and the prospectus included therein, as then
amended or supplemented, and from any documents incorporated by reference
therein of an untrue statement of a material fact or the omission to state
therein a material fact required to be stated therein or necessary to make the
statements therein not misleading (in the case of any such documents, in the
light of the circumstances existing at the time that such documents were filed
with the Commission under the Securities Exchange Act of 1934, as amended (the
"Exchange Act"), it being understood that the items contained in this clause (G)
may be in the form of a statement), (ii) its officers to execute and deliver all
customary documents and certificates and updates thereof requested by any
underwriters of the Securities or counsel for the Holders and (iii) its
independent public accountants and the independent public accountants with
respect to any other entity for which financial information is provided in the
Shelf Registration Statement to provide to the selling Holders of the Securities
and any underwriter therefor a comfort letter in customary form and covering
matters of the type customarily covered in comfort letters in connection with
primary underwritten offerings, subject to receipt of appropriate documentation
as contemplated, and only if permitted, by Statement of Auditing Standards No.
72.

     (p) The Company shall use its best efforts to take all other steps
necessary to effect the registration of the Securities covered by the Shelf
Registration Statement.

     3. REGISTRATION EXPENSES. The Company shall bear all fees and expenses
incurred in connection with the performance of its obligations under Sections

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1 and 2 hereof (including the reasonable fees and expenses, if any, of counsel
for the Initial Purchasers, incurred in connection with the Shelf Registration),
whether or not the Shelf Registration Statement is filed or becomes effective,
and shall bear or reimburse the Holders of the Securities covered by the Shelf
Registration for the reasonable fees and disbursements of one firm of counsel
designated by the Holders of a majority in principal amount of the Securities
covered by the Shelf Registration Statement (provided that Holders of Common
Stock issued upon the conversion of the Notes shall be deemed to be Holders of
the aggregate principal amount of Notes from which such Common Stock was
converted) to act as counsel for the Holders in connection therewith.

     4. INDEMNIFICATION. (a) The Company agrees to indemnify and hold harmless
each Holder and each person, if any, who controls such Holder within the meaning
of the Securities Act or the Exchange Act (each Holder and such controlling
persons are referred to collectively as the "Indemnified Parties") from and
against any losses, claims, damages or liabilities, joint or several, or any
actions in respect thereof (including, but not limited to, any losses, claims,
damages, liabilities or actions relating to purchases and sales of the
Securities) to which each Indemnified Party becomes subject under the Securities
Act, the Exchange Act or otherwise, insofar as such losses, claims, damages,
liabilities or actions arise out of or are based upon any untrue statement or
alleged untrue statement of a material fact contained in the Shelf Registration
Statement or Prospectus, including any document incorporated by reference
therein, or in any amendment or supplement thereto or in any preliminary
prospectus relating to the Shelf Registration, or arise out of, or are based
upon, the omission or alleged omission to state therein a material fact required
to be stated therein or necessary to make the statements therein not misleading,
and shall reimburse, as incurred, the Indemnified Parties for any legal or other
expenses reasonably incurred by them in connection with investigating or
defending any such loss, claim, damage, liability or action in respect thereof;
PROVIDED, HOWEVER, that (i) the Company shall not be liable in any such case to
the extent that such loss, claim, damage or liability arises out of or is based
upon any untrue statement or alleged untrue statement or omission or alleged
omission made in the Shelf Registration Statement or Prospectus or in any
amendment or supplement thereto or in any preliminary prospectus relating to the
Shelf Registration in reliance upon and in conformity with written information
pertaining to such Holder and furnished to the Company by or on behalf of such
Holder specifically for inclusion therein and (ii) with respect to any untrue
statement or omission or alleged untrue statement or omission made in any
preliminary prospectus relating to the Shelf Registration Statement, the
indemnity agreement contained in this subsection (a) shall not inure to the
benefit of any Holder from whom the person asserting any such losses, claims,
damages or liabilities purchased the Securities concerned, to the extent that a
prospectus relating to

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such Securities was required to be delivered by such Holder under the Securities
Act in connection with such purchase and any such loss, claim, damage or
liability of such Holder results from the fact that there was not sent or given
to such person, at or prior to the written confirmation of the sale of such
Securities to such person, a copy of the final prospectus if the Company had
previously furnished copies thereof to such Holder; PROVIDED FURTHER, HOWEVER,
that this indemnity agreement will be in addition to any liability which the
Company may otherwise have to such Indemnified Party.

     The Company shall also indemnify the underwriters, their officers and
directors and each person who controls such underwriters within the meaning of
the Securities Act or the Exchange Act to the same extent as provided above with
respect to the indemnification of the Holders if requested by such Holders.

     (b) Each Holder, severally and not jointly, will indemnify and hold
harmless the Company, its officers and directors and each person, if any, who
controls the Company within the meaning of the Securities Act or the Exchange
Act from and against any losses, claims, damages or liabilities or any actions
in respect thereof, to which the Company or any such controlling person may
become subject under the Securities Act, the Exchange Act or otherwise, insofar
as such losses, claims, damages, liabilities or actions arise out of or are
based upon any untrue statement or alleged untrue statement of a material fact
contained in a Shelf Registration Statement or prospectus or in any amendment or
supplement thereto or in any preliminary prospectus relating to a Shelf
Registration, or arise out of or are based upon the omission or alleged omission
to state therein a material fact necessary to make the statements therein not
misleading, but in each case only to the extent that the untrue statement or
omission or alleged untrue statement or omission was made in reliance upon and
in conformity with written information pertaining to such Holder and furnished
to the Company by or on behalf of such Holder specifically for inclusion
therein; and, subject to the limitation set forth immediately preceding this
clause, shall reimburse, as incurred, the Company for any legal or other
expenses reasonably incurred by the Company or any such controlling person in
connection with investigating or defending any loss, claim, damage, liability or
action in respect thereof. This indemnity agreement will be in addition to any
liability which such Holder may otherwise have to the Company or any of its
controlling persons.

     (c) Promptly after receipt by an indemnified party under this Section 4 of
notice of the commencement of any action or proceeding (including a governmental
investigation), such indemnified party will, if a claim in respect thereof is to
be made against the indemnifying party under this Section 4, notify the
indemnifying party of the

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commencement thereof; but the omission so to notify the indemnifying party will
not, in any event, relieve the indemnifying party from any obligations to any
indemnified party other than the indemnification obligation provided in
subsections (a) or (b) above. In case any such action is brought against any
indemnified party, and it notifies the indemnifying party of the commencement
thereof, the indemnifying party will be entitled to participate therein and, to
the extent that it may wish, jointly with any other indemnifying party similarly
notified, to assume the defense thereof, with counsel reasonably satisfactory to
such indemnified party (who shall not, except with the consent of the
indemnified party, be counsel to the indemnifying party), and after notice from
the indemnifying party to such indemnified party of its election so to assume
the defense thereof the indemnifying party will not be liable to such
indemnified party under this Section 4 for any legal or other expenses, other
than reasonable costs of investigation, subsequently incurred by such
indemnified party in connection with the defense thereof. No indemnifying party
shall, without the prior written consent of the indemnified party, effect any
settlement of any pending or threatened action in respect of which any
indemnified party is or could have been a party and indemnity could have been
sought hereunder by such indemnified party unless such settlement includes an
unconditional release of such indemnified party from all liability on any claims
that are the subject matter of such action.

     (d) If the indemnification provided for in this Section 4 is unavailable or
insufficient to hold harmless an indemnified party under subsections (a) or (b)
above, then each indemnifying party shall contribute to the amount paid or
payable by such indemnified party as a result of the losses, claims, damages or
liabilities (or actions in respect thereof) referred to in subsections (a) or
(b) above (i) in such proportion as is appropriate to reflect the relative
benefits received by the indemnifying party or parties on the one hand and the
indemnified party on the other from the registration of the Securities, pursuant
to the Shelf Registration, or (ii) if the allocation provided by the foregoing
clause (i) is not permitted by applicable law, in such proportion as is
appropriate to reflect not only the relative benefits referred to in clause (i)
above but also the relative fault of the indemnifying party or parties on the
one hand and the indemnified party on the other in connection with the
statements or omissions that resulted in such losses, claims, damages or
liabilities (or actions in respect thereof) as well as any other relevant
equitable considerations. The relative fault of the parties shall be determined
by reference to, among other things, whether the untrue or alleged untrue
statement of a material fact or the omission or alleged omission to state a
material fact relates to information supplied by the Company on the one hand or
such Holder or such other indemnified party, as the case may be, on the other,
and the parties' relative intent, knowledge, access to information and
opportunity to correct or prevent such statement or omission. The amount paid by
an indemnified party as a result of the losses, claims, damages or liabilities
referred to in the first sentence of this subsection (d) shall be deemed to
include any legal or other expenses reasonably

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incurred by such indemnified party in connection with investigating or defending
any action or claim which is the subject of this subsection (d). Notwithstanding
any other provision of this Section 4(d), the Holders shall not be required to
contribute any amount in excess of the amount by which the net proceeds received
by such Holders from the sale of the Securities pursuant to the Shelf
Registration Statement exceeds the amount of damages which such Holders have
otherwise been required to pay by reason of such untrue or alleged untrue
statement or omission or alleged omission. No person guilty of fraudulent
misrepresentation (within the meaning of Section 11(f) of the Securities Act)
shall be entitled to contribution from any person who was not guilty of such
fraudulent misrepresentation. For purposes of this paragraph (d), each person,
if any, who controls such indemnified party within the meaning of the Securities
Act or the Exchange Act shall have the same rights to contribution as such
indemnified party and each person, if any, who controls the Company within the
meaning of the Securities Act or the Exchange Act shall have the same rights to
contribution as the Company.

     (e) The agreements contained in this Section 4 shall survive the sale of
the Securities pursuant to the Shelf Registration Statement and shall remain in
full force and effect, regardless of any termination or cancellation of this
Agreement or any investigation made by or on behalf of any indemnified party.

     5. ADDITIONAL INTEREST UNDER CERTAIN CIRCUMSTANCES. (a) Additional interest
(the "Additional Interest") with respect to the Notes shall be assessed as
follows if any of the following events occur (each such event in clauses (i)
through (iii) below being herein called a "Registration Default"):

          (i) the Shelf Registration Statement has not been filed with the
     Commission by the 90th day after the first date of original issuance of the
     Notes;

         (ii) the Shelf Registration Statement has not been declared effective
     by the Commission by the 150th day after the first date of original
     issuance of the Notes; or

        (iii) the Shelf Registration Statement is declared effective but (A)
     the Shelf Registration Statement thereafter ceases to be effective; or (B)
     the Shelf Registration Statement or the Prospectus ceases to be usable in
     connection with resales of Transfer Restricted Securities (as defined
     below) during the periods specified herein because either (1) any event
     occurs as a result of which the Prospectus forming part of such Shelf
     Registration Statement would include any untrue statement of a material
     fact or omit to state any material fact necessary to

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     make the statements therein in the light of the circumstances under which
     they were made not misleading, or (2) it shall be necessary to amend such
     Shelf Registration Statement or supplement the related prospectus, to
     comply with the Securities Act or the Exchange Act or the respective rules
     thereunder.

     Additional Interest shall accrue on the Notes over and above the interest
set forth in the title of the Notes from and including the date on which any
such Registration Default shall occur, to but excluding the date on which all
such Registration Defaults have been cured, at a rate of 0.50% per annum.

     (b) A Registration Default referred to in Section 5(a)(iii)(B) shall be
deemed not to have occurred and be continuing in relation to the Shelf
Registration Statement or the Prospectus if (i) such Registration Default has
occurred solely as a result of (x) the filing of a post-effective amendment to
the Shelf Registration Statement to incorporate annual audited financial
information with respect to the Company where such post-effective amendment is
not yet effective and needs to be declared effective to permit Holders to use
the related prospectus or (y) other material events, with respect to the Company
that would need to be described in the Shelf Registration Statement or the
related prospectus and (ii) in the case of clause (y), the Company is proceeding
in good faith to amend or supplement the Shelf Registration Statement and
related prospectus to describe such events as required by paragraph 2(h) hereof;
PROVIDED, HOWEVER, that in any case if such Registration Default occurs for a
continuous period in excess of 90 days, Additional Interest shall be payable in
accordance with the above paragraph from the day such Registration Default
occurs until such Registration Default is cured.

     (c) Any amounts of Additional Interest due pursuant to Section 5(a) will be
payable in cash on the regular interest payment dates with respect to the Notes.
The amount of Additional Interest will be determined by multiplying the
applicable Additional Interest rate by the principal amount of the Notes,
further multiplied by a fraction, the numerator of which is the number of days
such Additional Interest rate was applicable during such period (determined on
the basis of a 360- day year comprised of twelve 30-day months), and the
denominator of which is 360. The indebtedness represented by the Additional
Interest shall be subordinated in right of payment to all existing and future
Senior Indebtedness (as defined in the Indenture) as and to the same extent as
the Notes.

     (d) "Transfer Restricted Securities" means each Security until (i) the date
on which such Security has been effectively registered under the Securities Act
and disposed of in accordance with the Shelf Registration Statement or (ii) the
date on which such Security is distributed to the public pursuant to Rule 144
under the Securities Act or is saleable pursuant to Rule 144(k) under the
Securities Act.

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     6. RULES 144 AND 144A. The Company shall use its best efforts to file the
reports required to be filed by it under the Securities Act and the Exchange Act
in a timely manner and, if at any time the Company is not required to file such
reports, it will, upon the request of any Holder, make publicly available other
information so long as necessary to permit sales of their securities pursuant to
Rules 144 and 144A. The Company covenants that it will take such further action
as any Holder may reasonably request, all to the extent required from time to
time to enable such Holder to sell Transfer Restricted Securities without
registration under the Securities Act within the limitations of the exemptions
provided by Rules 144 and 144A (including the requirements of Rule 144A(d)(4)).
The Company will provide a copy of this Agreement to prospective purchasers of
Securities identified to the Company by the Initial Purchaser upon request. Upon
the request of any Holder, the Company shall deliver to such Holder a written
statement as to whether it has complied with such requirements. Notwithstanding
the foregoing, nothing in this Section 6 shall be deemed to require the Company
to register any of its securities pursuant to the Exchange Act.

     7. UNDERWRITTEN REGISTRATIONS. If any of the Transfer Restricted Securities
covered by the Shelf Registration are to be sold in an underwritten offering,
the investment banker or investment bankers and manager or managers that will
administer the offering ("Managing Underwriters") will be selected by the
Company.

     No person may participate in any underwritten registration hereunder unless
such person (i) agrees to sell such person's Transfer Restricted Securities on
the basis reasonably provided in any underwriting arrangements approved by the
persons entitled hereunder to approve such arrangements and (ii) completes and
executes all questionnaires, powers of attorney, indemnities, underwriting
agreements and other documents reasonably required under the terms of such
underwriting arrangements.

     8. MISCELLANEOUS. (a) AMENDMENTS AND WAIVERS. The provisions of this
Agreement may not be amended, modified or supplemented, and waivers or consents
to departures from the provisions hereof may not be given, except by the Company
and the written consent of the Holders of a majority in principal amount of the
Securities (provided that Holders of Common Stock issued upon conversion of
Notes shall not be deemed Holders of Common Stock, but shall be deemed to be
Holders of the aggregate principal amount of Notes from which such Common Stock
was converted) affected by such amendment, modification, supplement, waiver or
consents.

                                       13
<PAGE>

     (b) NOTICES. All notices and other communications provided for or permitted
hereunder shall be made in writing by hand delivery, first-class mail, facsimile
transmission, or air courier which guarantees overnight delivery:

          (1) if to a Holder, at the most current address given by such Holder
     to the Company;

          (2) if to the Initial Purchasers:

              Credit Suisse First Boston Corporation
              Eleven Madison Avenue
              New York, NY 10010-3629
              Fax No.: (212) 325-8278
              Attention:  Transactions Advisory Group


                                       14
<PAGE>

     with a copy to:

              Cravath, Swaine & Moore
              Worldwide Plaza
              825 Eighth Avenue
              New York, NY 10019
              Fax No.:  (212) 474-3700
              Attention:  Kris Heinzelman, Esq.

          (3) if to the Company, at its address as follows:

              Affymetrix, Inc.
              3380 Central Expressway
              Santa Clara, CA 95051
              Fax No.: (408) 731-5000
              Attention: Vernon A. Norviel

     with a copy to:

              Sullivan & Cromwell
              1888 Century Park East
              Los Angles, CA 90067-1725
              Fax No.: (310) 712-8800
              Attention: Stanley F. Farrar, Esq.

     All such notices and communications shall be deemed to have been duly
given: at the time delivered by hand, if personally delivered; three business
days after being deposited in the mail, postage prepaid, if mailed; when receipt
is acknowledged by recipient's facsimile machine operator, if sent by facsimile
transmission; and on the day delivered, if sent by overnight air courier
guaranteeing next day delivery.

     (c) NO INCONSISTENT AGREEMENTS. The Company has not, as of the date hereof,
entered into, nor shall it, on or after the date hereof, without the prior
consent of CSFBC, enter into, any agreement with respect to its securities that
is inconsistent with the rights granted to the Holders herein or otherwise
conflicts with the provisions hereof.

     (d) SUCCESSORS AND ASSIGNS. This Agreement shall be binding upon the
Company and its successors and assigns.

                                       15
<PAGE>

     (e) COUNTERPARTS. This Agreement may be executed in any number of
counterparts and by the parties hereto in separate counterparts, each of which
when so executed shall be deemed to be an original and all of which taken
together shall constitute one and the same agreement.

     (f) HEADINGS. The headings in this Agreement are for convenience of
reference only and shall not limit or otherwise affect the meaning hereof.

     (g) GOVERNING LAW. THIS AGREEMENT SHALL BE GOVERNED BY, AND CONSTRUED IN
ACCORDANCE WITH, THE LAWS OF THE STATE OF NEW YORK WITHOUT REGARD TO PRINCIPLES
OF CONFLICTS OF LAWS.

     By the execution and delivery of this Agreement, the Company submits to the
nonexclusive jurisdiction of any federal or state court in the State of New
York.

     (h) SEVERABILITY. If any one or more of the provisions contained herein, or
the application thereof in any circumstance, is held invalid, illegal or
unenforceable, the validity, legality and enforceability of any such provision
in every other respect and of the remaining provisions contained herein shall
not be affected or impaired thereby.

     (i) SECURITIES HELD BY THE COMPANY. Whenever the consent or approval of
Holders of a specified percentage of principal amount of Securities is required
hereunder, Securities held by the Company or its affiliates (other than
subsequent Holders of Securities if such subsequent Holders are deemed to be
affiliates solely by reason of their holdings of such Securities)

<PAGE>

shall not be counted in determining whether such consent or approval was given
by the Holders of such required percentage.

     If the foregoing is in accordance with your understanding of our agreement,
please sign and return to the Company a counterpart hereof, whereupon this
instrument, along with all counterparts, will become a binding agreement among
the Initial Purchasers and the Company in accordance with its terms.


                                       Very truly yours,

                                       AFFYMETRIX, INC.


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

The foregoing Registration
Rights Agreement is hereby confirmed
and accepted as of the date first
above written.


CREDIT SUISSE FIRST BOSTON CORPORATION,
Acting on behalf of themselves and as
The Representative of the several Initial
Purchasers

CREDIT SUISSE FIRST BOSTON CORPORATION,



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