<PAGE>

                            STOCK PURCHASE AGREEMENT

Aurora Biosciences Corporation
11010 Torreyana Road
San Diego, California 92121

The undersigned (the "Investor"), hereby confirms its agreement with you as
follows:

1. This Stock Purchase Agreement (the "Agreement") is made as of the date set
forth below between Aurora Biosciences Corporation, a Delaware corporation (the
"Company"), and the Investor.

2. The Company has authorized the sale and issuance of up to
_______________________ shares (the "Shares") of common stock of the Company,
$.001 par value per share (the "Common Stock"), subject to adjustment by the
Company's Board of Directors, to certain investors in a private placement (the
"Offering").

3. The Company and the Investor agree that the Investor will purchase from
the Company and the Company will issue and sell to the Investor ____________
shares, for a purchase price of $_________________ per share, or an aggregate
purchase price of $____________________, pursuant to the Terms and Conditions
for Purchase of Shares attached hereto as Annex I and incorporated herein by
this reference as if fully set forth herein. Unless otherwise requested by
the Investor, certificates representing the Shares purchased by the Investor
will be registered in the Investor's name and address as set forth below.

4. The Investor represents that, except as set forth below, (a) it has had no
position, office or other material relationship within the past three years with
the Company or its affiliates, (b) neither it, nor any group of which it is a
member or to which it is related, beneficially owns (including the right to
acquire or vote) any securities of the Company and (c) it has no direct or
indirect affiliation or association with any NASD member. Exceptions:


--------------------------------------------------------------------------------
        (If no exceptions, write "none." If left blank, response will be
                             deemed to be "none.")

Please confirm that the foregoing correctly sets forth the agreement between us
by signing in the space provided below for that purpose.

                                          DATED AS OF: ___________________, 2000

                                          --------------------------------------
                                          "INVESTOR"

                                          By:
                                             -----------------------------------
                                          Print Name:
                                                     ---------------------------
                                          Title:
                                                --------------------------------
                                          Address:
                                                  ------------------------------

                                          --------------------------------------
AGREED AND ACCEPTED:
AURORA BIOSCIENCES CORPORATION

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


<PAGE>



                                     ANNEX I

                   TERMS AND CONDITIONS FOR PURCHASE OF SHARES

         1. AUTHORIZATION AND SALE OF THE SHARES. Subject to the terms and
conditions of this Agreement, the Company has authorized the sale of the Shares.

         2. AGREEMENT TO SELL AND PURCHASE THE SHARES; SUBSCRIPTION DATE.

                  2.1 At the Closing (as defined in Section 3), the Company will
sell to the Investor, and the Investor will purchase from the Company, upon the
terms and conditions hereinafter set forth, the number of Shares set forth on
the signature page to which these Terms and Conditions for Purchase of Shares
are attached as Annex I (the "Signature Page") at the purchase price set forth
on such Signature Page.

                  2.2 The Company proposes to enter into this same form of Stock
Purchase Agreement with certain other investors (the "Other Investors") and
expects to complete sales of Shares to them. (The Investor and the Other
Investors are hereinafter sometimes collectively referred to as the "Investors,"
and this Agreement and the Stock Purchase Agreements executed by the Other
Investors are hereinafter sometimes collectively referred to as the
"Agreements.") The Company will accept executed Agreements from Investors for
the purchase of Shares commencing upon the date on which the Company provides
the Investors with the proposed purchase price per Share and concluding upon the
date (the "Subscription Date") on which the Company has (i) executed Agreements
with Investors each for the purchase of Shares in the amount of at least
$10,000,000 and (ii) notified Deutsche Bank Securities, Inc. (in its capacity as
Placement Agent for the Shares, the "Placement Agent") in writing that it is no
longer accepting Agreements from Investors for the purchase of Shares.

                  2.3 Investor acknowledges that the Company intends to pay the
Placement Agent a fee in respect of the sale of Shares to the Investor.

         3. DELIVERY OF THE SHARES AT CLOSING. The completion of the purchase
and sale of the Shares (the "Closing") shall occur on Thursday, February 10,
2000 or, at the Company's discretion, on such other date within ten (10) days
thereafter at a place and time (the "Closing Date") to be specified by the
Company and the Placement Agent, and of which the Investors will be notified in
advance by the Placement Agent. At the Closing, (i) the Company shall deliver to
the Investor one or more stock certificates representing the number of Shares
set forth on the signature page hereto, each such certificate to be registered
in the name of the Investor or, if so indicated on the Stock Certificate
Questionnaire attached hereto as Exhibit A, in the name of a nominee designated
by the Investor and (ii) the Investor shall deliver immediately available funds
in the amount of the aggregate purchase price for the Shares by wire transfer to
an account designated by the Placement Agent.

         The Company's obligation to issue the Shares to the Investor shall be
subject to the following conditions, any one or more of which may be waived by
the Company: (a) receipt by the Company of the purchase price for the Shares
being purchased hereunder as set forth on the Signature Page hereto; (b)
completion of purchases and sales under the Agreements with the


                                       1
<PAGE>

Other Investors; and (c) the accuracy of the representations and warranties
made by the Investors and the fulfillment of those undertakings of the
Investors to be fulfilled prior to the Closing.

         The Investor's obligation to purchase the Shares shall be subject to
the following conditions, any one or more of which may be waived by the
Investor: (a) Investors shall have executed Agreements each for the purchase of
Shares in the amount of at least $10,000,000; and (b) the satisfaction of all of
the conditions set forth in the Engagement Letter between the Company and the
Placement Agent. Subject to clause (a) above, the Investor's obligations are
expressly not conditioned on the purchase by any or all of the other Investors
of the Shares that they have agreed to purchase from the Company.

         4. REPRESENTATIONS, WARRANTIES AND COVENANTS OF THE COMPANY. Except as
otherwise described in the Company's regular reports on Form 10-Q and 10-K as
filed by the Company with the Securities and Exchange Commission in 1999 (the
"SEC Documents"), in the Company's press releases since September 30, 1999, and
in the other Proprietary Information disclosed by the Company to the Investor in
contemplation of this offering (including the documents incorporated by
reference therein, the "Company Information"), which qualifies the following
representations and warranties in their entirety, the Company hereby represents
and warrants to, and covenants with, the Investor, as follows:

                  4.1 ORGANIZATION. The Company is duly incorporated and
validly existing in good standing under the laws of the jurisdiction of its
organization. The Company has full power and authority to own, operate and
occupy its properties and to conduct its business as presently conducted and
is registered or qualified to do business and in good standing in each
jurisdiction in which it owns or leases property or transacts business and
where the failure to be so qualified would have a material adverse effect
upon the business, financial condition, properties or operations of the
Company ("Material Adverse Effect"), and no proceeding has been instituted in
any such jurisdiction revoking, limiting or curtailing, or seeking to revoke,
limit or curtail, such power and authority or qualification.

                  4.2 DUE AUTHORIZATION. The Company has all requisite power
and authority to execute, deliver and perform its obligations under the
Agreements, and the Agreements have been duly authorized and validly executed
and delivered by the Company and constitute legal, valid and binding
agreements of the Company enforceable against the Company in accordance with
their terms, except as rights to indemnity and contribution may be limited by
state or federal securities laws or the public policy underlying such laws,
except as enforceability may be limited by applicable bankruptcy, insolvency,
reorganization, moratorium or similar laws affecting creditors' and
contracting parties' rights generally and except as enforceability may be
subject to general principles of equity (regardless of whether such
enforceability is considered in a proceeding in equity or at law).

                  4.3 NON-CONTRAVENTION. The execution and delivery of the
Agreements, the issuance and sale of the Shares to be sold by the Company under
the Agreements, the fulfillment of the terms of the Agreements and the
consummation of the transactions contemplated thereby will not (A) conflict with
or constitute a violation of, or default (with the passage of time or otherwise)
under, (i) any material bond, debenture, note or other evidence of indebtedness,
or any material lease, contract, indenture, mortgage, deed of trust, loan
agreement, joint venture or


                                       2
<PAGE>

other agreement or instrument to which the Company is a party or by which it
or its property is bound, where such conflict, violation or default is likely
to result in a Material Adverse Effect, (ii) the charter, by-laws or other
organizational documents of the Company, or (iii) any law, administrative
regulation, ordinance or order of any court or governmental agency,
arbitration panel or authority binding upon the Company or its property,
where such conflict, violation or default is likely to result in a Material
Adverse Effect, or (B) result in the creation or imposition of any lien,
encumbrance, claim, security interest or restriction whatsoever upon any of
the material properties or assets of the Company or an acceleration of
indebtedness pursuant to any obligation, agreement or condition contained in
any material bond, debenture, note or any other evidence of indebtedness or
any material indenture, mortgage, deed of trust or any other agreement or
instrument to which the Company is a party or by which it is bound or to
which any of the property or assets of the Company is subject. No consent,
approval, authorization or other order of, or registration, qualification or
filing with, any regulatory body, administrative agency, or other
governmental body in the United States is required for the execution and
delivery of the Agreements and the valid issuance and sale of the Shares to
be sold pursuant to the Agreements, other than such as have been made or
obtained, and except for any securities filings required to be made under
federal or state securities laws.

                  4.4 CAPITALIZATION. The capitalization of the Company is
described in the Company's SEC Documents. The Company has not issued any capital
stock since September 30, 1999 other than pursuant to employee benefit plans
disclosed in the Company's SEC Documents. The Shares to be sold pursuant to the
Agreements have been duly authorized, and when issued and paid for in accordance
with the terms of the Agreements, will be duly and validly issued, fully paid
and nonassessable. The outstanding shares of capital stock of the Company have
been duly and validly issued and are fully paid and nonassessable, have been
issued in compliance with all federal and state securities laws, and were not
issued in violation of any preemptive rights or similar rights to subscribe for
or purchase securities. Except as set forth in or contemplated by the Company's
SEC Documents, there are no outstanding rights (including, without limitation,
preemptive rights), warrants or options to acquire, or instruments convertible
into or exchangeable for, any unissued shares of capital stock or other equity
interest in the Company, or any contract, commitment, agreement, understanding
or arrangement of any kind to which the Company is a party and relating to the
issuance or sale of any capital stock of the Company, any such convertible or
exchangeable securities or any such rights, warrants or options. Without
limiting the foregoing, no preemptive right, co-sale right, registration right,
right of first refusal or other similar right exists with respect to the
issuance and sale of the Shares. Except as disclosed in the Company's SEC
Documents, there are no stockholders agreements, voting agreements or other
similar agreements with respect to the Common Stock to which the Company is a
party.

                  4.5 LEGAL PROCEEDINGS. There is no material legal or
governmental proceeding pending to which the Company is a party or of which the
business or property of the Company is subject that is not disclosed in the
Company's SEC Documents.

                  4.6 NO VIOLATIONS. The Company is not in violation of its
charter, bylaws or other organizational document, or in violation of any law,
administrative regulation, ordinance or order of any court or governmental
agency, arbitration panel or authority applicable to the Company, which
violation, individually or in the aggregate, would be reasonably likely to
have a


                                       3
<PAGE>

Material Adverse Effect, or is in default (and there exists no condition
which, with the passage of time or otherwise, would constitute a default) in
the performance of any material bond, debenture, note or any other evidence
of indebtedness in any indenture, mortgage, deed of trust or any other
material agreement or instrument to which the Company is a party or by which
the Company is bound or by which the property of the Company is bound, which
would be reasonably likely to have a Material Adverse Effect.

                  4.7 GOVERNMENTAL PERMITS, ETC. With the exception of the
matters which are dealt with separately in Sections 4.1, 4.12, and 4.13, the
Company has all necessary franchises, licenses, certificates and other
authorizations from any foreign, federal, state or local government or
governmental agency, department or body that are currently necessary for the
operation of the business of the Company as currently conducted except where the
failure to currently possess could not reasonably be expected to have a Material
Adverse Effect.

                  4.8 INTELLECTUAL PROPERTY.

                     (a) The Company has ownership or license or legal right
to use all patent, copyright, trade secret, trademark, customer lists,
designs, manufacturing or other processes, computer software, systems, data
compilation, research results or other proprietary rights used in the
business of the Company and material to the Company (collectively,
"Intellectual Property") other than Intellectual Property generally available
on commercial terms from other sources. All of such patents, trademarks and
registered copyrights have been duly registered in, filed in or issued by the
United States Patent and Trademark Office, the United States Register of
Copyrights or the corresponding offices of other jurisdictions and have been
maintained and renewed in accordance with all applicable provisions of law
and administrative regulations in the United States and all such
jurisdictions.

                     (b) All material licenses or other material agreements
under which (i) the Company is granted rights in Intellectual Property, other
than Intellectual Property generally available on commercial terms from other
sources, and (ii) the Company has granted rights to others in Intellectual
Property owned or licensed by the Company, are in full force and effect and,
to the knowledge of the Company, there is no material default by the Company
thereto.

                     (c) The Company believes it has taken all steps required
in accordance with sound business practice and business judgment to establish
and preserve its ownership of all material copyright, trade secret and other
proprietary rights with respect to its products and technology.

                     (d) To the knowledge of the Company, the present
business, activities and products of the Company do not infringe any
intellectual property of any other person, except where such infringement
would not have a Material Adverse Effect on the Company. Except as described
in the Company's SEC Documents, no proceeding charging the Company with
infringement of any adversely held Intellectual Property has been filed. To
the Company's knowledge, there exists no unexpired patent or patent
application which includes claims that would be infringed by or otherwise
have a Material Adverse Effect on the Company. To the knowledge of the
Company, the Company is not making unauthorized use of any confidential
information or trade secrets of any person. Neither the Company nor, to the
knowledge of the


                                       4
<PAGE>

Company, any of its employees have any agreements or arrangements with any
persons other than the Company related to confidential information or trade
secrets of such persons or restricting any such employee's engagement in
business activities of any nature. To the Company's knowledge, the activities
of the Company or any of its employees on behalf of the Company do not
violate any such agreements or arrangements known to the Company which any
such employees have with other persons, if any.

                     (e) No proceedings have been instituted or are pending
which challenge in a material manner the rights of the Company in respect to
the Company's right to the use of the Intellectual Property. The Company has
the right to use, free and clear of material claims or rights of other
persons, all of its customer lists, designs, computer software, systems, data
compilations, and other information that are required for its products or its
business as presently conducted.

                  4.9 FINANCIAL STATEMENTS. The financial statements of the
Company and the related notes contained in the Company's SEC Documents
present fairly, in accordance with generally accepted accounting principles,
the financial position of the Company as of the dates indicated, and the
results of its operations and cash flows for the periods therein specified.
Such financial statements (including the related notes) have been prepared in
accordance with generally accepted accounting principles applied on a
consistent basis throughout the periods therein specified, except as
disclosed in the Company's SEC Documents.

                  4.10 NO MATERIAL ADVERSE CHANGE. Except as disclosed in the
Company's press releases or other Proprietary Information provided to the
Investor in contemplation of this Offering, since September 30, 1999, there
has not been (i) any Material Adverse Effect affecting the Company, (ii) any
obligation, direct or contingent, that is material to the Company considered
as one enterprise, incurred by the Company, except obligations incurred in
the ordinary course of business, (iii) any dividend or distribution of any
kind declared, paid or made on the capital stock of the Company, or (iv) any
loss or damage (whether or not insured) to the physical property of the
Company which has been sustained which has a Material Adverse Effect.

                  4.11 NASDAQ COMPLIANCE. The Company's Common Stock is
registered pursuant to Section 12(g) of the Exchange Act and is listed on The
Nasdaq National Market (the "Nasdaq Stock Market"), and the Company has taken
no action designed to, or likely to have the effect of, terminating the
registration of the Common Stock under the Exchange Act or delisting the
Common Stock from the Nasdaq Stock Market.

                  4.12 REPORTING STATUS. The Company has filed in a timely
manner all documents that the Company was required to file under the
Securities Exchange Act of 1934, as amended (the "Exchange Act"), during the
12 months preceding the date of this Agreement. The following documents
complied in all material respects with the SEC's requirements as of their
respective filing dates, and the information contained therein as of the date
thereof did not contain an 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 where they were made
not misleading:


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<PAGE>

                     (a) The Company's Annual Report on Form 10-K for the
year ended December 31, 1998 (the "10-K");

                     (b) The Company's Quarterly Reports on Form 10-Q for
each of the quarters ended March 31, 1999, June 30, 1999 and September 30,
1999; and

                     (c) All other documents, if any, filed by the Company
with the Securities and Exchange Commission since December 31, 1998 pursuant to
the reporting requirements of the Exchange Act.

                  4.13 LISTING. The Company shall comply with all
requirements of the National Association of Securities Dealers, Inc. with
respect to the issuance of the Shares and the listing thereof on the Nasdaq
Stock Market.

                  4.14 FOREIGN CORRUPT PRACTICES. Neither the Company nor, to
the knowledge of the Company, any agent or other person acting on behalf of
the Company, have (i) directly or indirectly, used any corporate funds for
unlawful contributions, gifts, entertainment or other unlawful expenses
related to foreign or domestic political activity, (ii) made any unlawful
payment to foreign or domestic government officials or employees or to
foreign or domestic political parties or campaigns from corporate funds,
(iii) failed to disclose fully any contribution made by the Company or made
by any person acting on its behalf and of which the Company is aware in
violation of law or (iv) violated in any material respect any provision of
the Foreign Corrupt Practices Act of 1977, as amended.

                  4.15 NO MANIPULATION OF STOCK. The Company has not taken and
will not, in violation of applicable law, take, any action outside the ordinary
course of business designed to or that might reasonably be expected to cause or
result in unlawful manipulation of the price of the Common Stock to facilitate
the sale or resale of the Shares.

                  4.16 ACCOUNTANTS. Ernst & Young LLP, who the Company expects
will express their opinion with respect to the financial statements to be
incorporated by reference from the Company's Annual Report on Form 10-K for the
year ended December 31, 1999 into the Registration Statement (as defined below)
and the Prospectus which forms a part thereof, are independent accountants as
required by the Securities Act and the rules and regulations promulgated
thereunder (the "Rules and Regulations").

                  4.17 CONTRACTS. The contracts described in the SEC Documents
or incorporated by reference therein that are material to the Company are in
full force and effect on the date hereof, and neither the Company nor, to the
Company's knowledge, any other party to such contracts is in breach of or
default under any of such contracts which would have a Material Adverse Effect.

                  4.18 TAXES. The Company has filed all necessary federal, state
and foreign income and franchise tax returns and has paid or accrued all taxes
shown as due thereon, and the Company has no knowledge of a tax deficiency which
has been or might be asserted or threatened against it which would have a
Material Adverse Effect.


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<PAGE>

                  4.19 TRANSFER TAXES. On the Closing Date, all stock
transfer or other taxes (other than income taxes) which are required to be
paid in connection with the sale and transfer of the Shares to be sold to the
Investor hereunder will be, or will have been, fully paid or provided for by
the Company and all laws imposing such taxes will be or will have been fully
complied with.

                  4.20 INVESTMENT COMPANY. The Company is not an "investment
company" or an "affiliated person" of, or "promoter" or "principal
underwriter" for an investment company, within the meaning of the Investment
Company Act of 1940, as amended.

                  4.21 INSURANCE. The Company maintains and will continue to
maintain insurance of the types and in the amounts that the Company
reasonably believes is adequate for its business, including, but not limited
to, insurance covering all real and personal property owned or leased by the
Company against theft, damage, destruction, acts of vandalism and all other
risks customarily insured against by similarly situated companies, all of
which insurance is in full force and effect.

                  4.22 LEGAL OPINION. The Company shall cause to be delivered
to the Investors and the Placement Agent by counsel to the Company a
customary legal opinion pertaining to Rule 10b-5 under the Securities
Exchange Act of 1934 and to the availability of an exemption from the
registration provisions of the Securities Act.

                  4.23 OFFERING MATERIALS. Other than the SEC Documents (the
"Offering Materials"), the Company has not distributed and will not
distribute prior to the Closing Date any offering material in connection with
the offering and sale of the Shares. The Company has not in the past nor will
it hereafter take any action independent of the Placement Agent to sell,
offer for sale or solicit offers to buy any securities of the Company which
would bring the offer, issuance or sale of the Shares, as contemplated by
this Agreement, within the provisions of Section 5 of the Securities Act,
unless such offer, issuance or sale was or shall be within the exemptions of
Section 4 of the Securities Act.

                  4.24 DISCLOSURE. The information contained in the SEC
Documents as of the date of such information did not contain an 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.

         5. REPRESENTATIONS, WARRANTIES AND COVENANTS OF THE INVESTOR.

                  5.1 The Investor represents and warrants to, and covenants
with, the Company that: (i) the Investor is an "accredited investor" as
defined in Regulation D under the Securities Act and the Investor is also
knowledgeable, sophisticated and experienced in making, and is qualified to
make decisions with respect to, investments in shares presenting an
investment decision like that involved in the purchase of the Shares,
including investments in securities issued by the Company and investments in
comparable companies, and has requested, received, reviewed and considered
all information it deemed relevant in making an informed decision to purchase
the Shares; (ii) the Investor is acquiring the number of Shares set forth on
the Signature Page hereto in the ordinary course of its business and for its
own account for investment only


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<PAGE>

and with no present intention of distributing any of such Shares or any
arrangement or understanding with any other persons regarding the
distribution of such Shares; (iii) the Investor will not, directly or
indirectly, offer, sell, pledge, transfer or otherwise dispose of (or solicit
any offers to buy, purchase or otherwise acquire or take a pledge of) any of
the Shares except in compliance with the Securities Act, applicable state
securities laws and the respective rules and regulations promulgated
thereunder; (iv) the Investor has answered all questions on the Signature
Page hereto and the Investor Questionnaire attached hereto as Exhibit B for
use in preparation of the Registration Statement and the answers thereto are
true and correct as of the date hereof and will be true and correct as of the
Closing Date; (v) the Investor will notify the Company immediately of any
change in any of such information until such time as the Investor has sold
all of its Shares or until the Company is no longer required to keep the
Registration Statement effective; and (vi) the Investor has, in connection
with its decision to purchase the number of Shares set forth on the signature
page hereto, relied only upon the Company Information provided to the
Investor by the Company in contemplation of this offering and the
representations and warranties of the Company contained herein. Investor
understands that its acquisition of the Shares has not been registered under
the Securities Act of 1933, as amended (the "Securities Act"), or registered
or qualified under any state securities law in reliance on specific
exemptions therefrom, which exemptions may depend upon, among other things,
the bona fide nature of the Investor's investment intent as expressed herein.
Investor has completed or caused to be completed and delivered to the Company
the Investor Questionnaire attached hereto Exhibit B, which questionnaire is
true and correct in all material respects.

                  5.2 The Investor acknowledges, represents and agrees that
no action has been or will be taken in any jurisdiction outside the United
States by the Company or the Placement Agent that would permit an offering of
the Shares, or possession or distribution of offering materials in connection
with the issue of the Shares, in any jurisdiction outside the United States
where action for that purpose is required. Each Investor outside the United
States will comply with all applicable laws and regulations in each foreign
jurisdiction in which it purchases, offers, sells or delivers Shares or has
in its possession or distributes any offering material, in all cases at its
own expense. The Placement Agent is not authorized to make any representation
or use any information in connection with the issue, placement, purchase and
sale of the Shares.

                  5.3 The Investor hereby covenants with the Company not to
make any sale of the Shares without complying with the provisions of this
Agreement, including Section 7.2 hereof, and without effectively causing the
prospectus delivery requirement under the Securities Act to be satisfied, and
the Investor acknowledges that the certificates evidencing the Shares will be
imprinted with a legend that prohibits their transfer except in accordance
therewith. The Investor acknowledges that there may occasionally be times
when the Company, based on the advice of its counsel, determines that it must
suspend the use of the Prospectus forming a part of the Registration
Statement until such time as an amendment to the Registration Statement has
been filed by the Company and declared effective by the SEC or until the
Company has amended or supplemented such Prospectus.

                  5.4 The Investor further represents and warrants to, and
covenants with, the Company that (i) the Investor has full right, power,
authority and capacity to enter into this Agreement and to consummate the
transactions contemplated hereby and has taken all necessary action to
authorize the execution, delivery and performance of this Agreement, and (ii)
this


                                       8
<PAGE>

Agreement constitutes a valid and binding obligation of the Investor
enforceable against the Investor in accordance with its terms, except as
enforceability may be limited by applicable bankruptcy, insolvency,
reorganization, moratorium or similar laws affecting creditors' and
contracting parties' rights generally and except as enforceability may be
subject to general principles of equity (regardless of whether such
enforceability is considered in a proceeding in equity or at law) and except
as the indemnification agreements of the Investors herein may be legally
unenforceable.

                  5.5 Investor will not, prior to the effectiveness of the
Registration Statement, sell, offer to sell, solicit offers to buy, dispose
of, loan, pledge or grant any right with respect to (collectively, a
"Disposition"), the Common Stock of the Company, nor will Investor engage in
any hedging or other transaction which is designed to or could reasonably be
expected to lead to or result in a Disposition of Common Stock of the Company
by the Investor or any other person or entity. Such prohibited hedging or
other transactions would include, without limitation, effecting any short
sale or having in effect any short position (whether or not such sale or
position is against the box and regardless of when such position was entered
into) or any purchase, sale or grant of any right (including, without
limitation, any put or call option) with respect to the Common Stock of the
Company or with respect to any security (other than a broad-based market
basket or index) that includes, relates to or derives any significant part of
its value from the Common Stock of the Company.

                  5.6 The Investor understands that nothing in this Agreement
or any other materials presented to the Investor in connection with the
purchase and sale of the Shares constitutes legal, tax or investment advice.
The Investor has consulted such legal, tax and investment advisors as it, in
its sole discretion, has deemed necessary or appropriate in connection with
its purchase of Shares.

         6. SURVIVAL OF REPRESENTATIONS, WARRANTIES AND AGREEMENTS.
Notwithstanding any investigation made by any party to this Agreement or by
the Placement Agent, all covenants, agreements, representations and
warranties made by the Company and the Investor herein shall survive the
execution of this Agreement, the delivery to the Investor of the Shares being
purchased and the payment therefor.

         7. REGISTRATION OF THE SHARES; COMPLIANCE WITH THE SECURITIES ACT.

                  7.1 REGISTRATION PROCEDURES AND EXPENSES. The Company shall:

                     (a) subject to receipt of necessary information from the
Investors, prepare and file with the SEC, as soon as practicable, but in no
event later than thirty (30) days after the Closing Date, a registration
statement on Form S-3 (the "Registration Statement") to enable the resale of
the Shares by the Investors from time to time through the automated quotation
system of the Nasdaq Stock Market or in privately-negotiated transactions;

                     (b) use its reasonable efforts, subject to receipt of
necessary information from the Investors, to cause the Registration Statement
to become effective as soon as practicable, but in no event later than ninety
(90) days after the Registration Statement is filed by the Company.
Notwithstanding the foregoing, if the Registration Statement is not declared


                                       9
<PAGE>

effective by June 15, 2000 and does not remain effective for 45 continuous
days thereafter, the Investor shall be entitled to a stock dividend in the
amount of 5% of the Shares purchased by such Investor hereunder.

                     (c) use its reasonable efforts to prepare and file with
the SEC such amendments and supplements to the Registration Statement and the
Prospectus used in connection therewith as may be necessary to keep the
Registration Statement current and effective for a period not exceeding, with
respect to each Investor's Shares purchased hereunder, the earlier of (i) the
second anniversary of the Closing Date, (ii) the date on which the Investor
may sell all Shares then held by the Investor without restriction by the
volume limitations of Rule 144(e) of the Securities Act or (iii) such time as
all Shares purchased by such Investor in this Offering have been sold
pursuant to a registration statement.

                     (d) furnish to the Placement Agent and to the Investor
with respect to the Shares registered under the Registration Statement such
number of copies of the Registration Statement, Prospectuses and Preliminary
Prospectuses in conformity with the requirements of the Securities Act and
such other documents as the Investor may reasonably request, in order to
facilitate the public sale or other disposition of all or any of the Shares
by the Investor, provided, however, that the obligation of the Company to
deliver copies of Prospectuses or Preliminary Prospectuses to the Investor
shall be subject to the receipt by the Company of reasonable assurances from
the Investor that the Investor will comply with the applicable provisions of
the Securities Act and of such other securities or blue sky laws as may be
applicable in connection with any use of such Prospectuses or Preliminary
Prospectuses;

                     (e) file documents required of the Company for normal
blue sky clearance in states specified in writing by the Investor, provided,
however, that the Company shall not be required to qualify to do business or
consent to service of process in any jurisdiction in which it is not now so
qualified or has not so consented;

                     (f) bear all expenses in connection with the procedures
in paragraph (a) through (e) of this Section 7.1 and the registration of the
Shares pursuant to the Registration Statement; and

                     (g) advise the Investors, promptly after it shall
receive notice or obtain knowledge of the issuance of any stop order by the
SEC delaying or suspending the effectiveness of the Registration Statement or
of the initiation of any proceeding for that purpose; and it will promptly
use its commercially reasonable efforts to prevent the issuance of any stop
order or to obtain its withdrawal at the earliest possible moment if such
stop order should be issued.

                     (h) With a view to making available to the Investor the
benefits of Rule 144 (or its successor rule) and any other rule or regulation
of the SEC that may at any time permit the Investor to sell Shares to the
public without registration, the Company covenants and agrees to: (i) make
and keep public information available, as those terms are understood and
defined in Rule 144, until the earlier of (A) such date as all of the
Investor's Shares may be resold pursuant to Rule 144(k) or any other rule of
similar effect or (B) such date as all of the Investor's Shares shall have
been resold; (ii) file with the SEC in a timely manner all reports and other
documents required of the Company under the Securities Act and under the
Exchange Act;


                                       10
<PAGE>

and (iii) furnish to the Investor upon request, as long as the Investor owns
any Shares, (A) a written statement by the Company that it has complied with
the reporting requirements of the Securities Act and the Exchange Act, (B) a
copy of the Company's most recent Annual Report on Form 10-K or Quarterly
Report on Form 10-Q, and (C) such other information as may be reasonably
requested in order to avail the Investor of any rule or regulation of the SEC
that permits the selling of any such Shares without registration.

         It shall be a condition precedent to the obligations of the Company
to take any action pursuant to this Section 7.1 that the Investor shall
furnish to the Company such information regarding itself, the Shares to be
sold by Investor, and the intended method of disposition of such securities
as shall be required to effect the registration of the Shares.

         The Company understands that the Investor disclaims being an
underwriter, but the Investor being deemed an underwriter by the SEC shall
not relieve the Company of any obligations it has hereunder, provided,
however, that if the Company receives notification from the SEC that the
Investor is deemed an underwriter, then the period by which the Company is
obligated to submit an acceleration request to the SEC shall be extended to
the earlier of (i) the 90th day after such SEC notification, or (ii) 120 days
after the initial filing of the Registration Statement with the SEC.

                  7.2 TRANSFER OF SHARES AFTER REGISTRATION; SUSPENSION.

                     (a) The Investor agrees that it will not effect any
Disposition of the Shares or its right to purchase the Shares that would
constitute a sale within the meaning of the Securities Act except as
contemplated in the Registration Statement referred to in Section 7.1 and as
described below, and that it will promptly notify the Company of any changes
in the information set forth in the Registration Statement regarding the
Investor or its plan of distribution.

                     (b) Except in the event that paragraph (c) below
applies, the Company shall: (i) if deemed necessary by the Company, prepare
and file from time to time with the SEC a post-effective amendment to the
Registration Statement or a supplement to the related Prospectus or a
supplement or amendment to any document incorporated therein by reference or
file any other required document so that such Registration Statement will not
contain an 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 not misleading, and so that, as thereafter delivered to purchasers of
the Shares being sold thereunder, such Prospectus will not contain an 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; (ii) provide the
Investor copies of any documents filed pursuant to Section 7.2(b)(i); and
(iii) inform each Investor that the Company has complied with its obligations
in Section 7.2(b)(i) (or that, if the Company has filed a post-effective
amendment to the Registration Statement which has not yet been declared
effective, the Company will notify the Investor to that effect, will use its
reasonable efforts to secure the effectiveness of such post-effective
amendment as promptly as possible and will promptly notify the Investor
pursuant to Section 7.2(b)(i) hereof when the amendment has become effective).



                                      11
<PAGE>

                     (c) Subject to paragraph (d) below, in the event: (i) of
any request by the SEC or any other federal or state governmental authority
during the period of effectiveness of the Registration Statement for
amendments or supplements to a Registration Statement or related Prospectus
or for additional information; (ii) of the issuance by the SEC or any other
federal or state governmental authority of any stop order suspending the
effectiveness of a Registration Statement or the initiation of any
proceedings for that purpose; (iii) of the receipt by the Company of any
notification with respect to the suspension of the qualification or exemption
from qualification of any of the Shares for sale in any jurisdiction or the
initiation of any proceeding for such purpose; or (iv) of any event or
circumstance which necessitates the making of any changes in the Registration
Statement or Prospectus, or any document incorporated or deemed to be
incorporated therein by reference, so that, in the case of the Registration
Statement, it will not contain any untrue statement of a material fact or any
omission to state a material fact required to be stated therein or necessary
to make the statements therein not misleading, and that in the case of the
Prospectus, it will not contain any untrue statement of a material fact or
any omission to state a material fact required to be stated therein or
necessary to make the statements therein, in the light of the circumstances
under which they were made, not misleading; then the Company shall deliver a
certificate in writing to the Investor (the "Suspension Notice") to the
effect of the foregoing and, upon receipt of such Suspension Notice, the
Investor will refrain from selling any Shares pursuant to the Registration
Statement (a "Suspension") until the Investor's receipt of copies of a
supplemented or amended Prospectus prepared and filed by the Company, or
until it is advised in writing by the Company that the current Prospectus may
be used, and has received copies of any additional or supplemental filings
that are incorporated or deemed incorporated by reference in any such
Prospectus. In the event of any Suspension, the Company will use its
reasonable efforts to cause the use of the Prospectus so suspended to be
resumed as soon as reasonably practicable within 20 business days after
delivery of a Suspension Notice to the Investors. In addition to and without
limiting any other remedies (including, without limitation, at law or at
equity) available to the Investor, the Investor shall be entitled to specific
performance in the event that the Company fails to comply with the provisions
of this Section 7.2(c).

                     (d) Notwithstanding the foregoing paragraphs of this
Section 7.2, the Investor shall not be prohibited from selling Shares under
the Registration Statement as a result of Suspensions on more than three
occasions of not more than 30 days each in any twelve month period, unless,
in the good faith judgment of the Company's Board of Directors, upon advice
of counsel, the sale of Shares under the Registration Statement in reliance
on this paragraph 7.2(d) would be reasonably likely to cause a violation of
the Securities Act or the Exchange Act and result in potential liability to
the Company.

                     (e) Provided that a Suspension is not then in effect the
Investor may sell Shares under the Registration Statement, provided that it
arranges for delivery of a current Prospectus to the transferee of such
Shares. Upon receipt of a request therefor, the Company has agreed to provide
an adequate number of current Prospectuses to the Investor and to supply
copies to any other parties requiring such Prospectuses.

                     (f) In the event of a sale of Shares by the Investor,
the Investor must also deliver to the Company's transfer agent, with a copy
to the Company, a Certificate of


                                       12
<PAGE>

Subsequent Sale substantially in the form attached hereto as Exhibit C, so
that the shares may be properly transferred.

                  7.3 INDEMNIFICATION. For the purpose of this Section 7.3:

                     (a) the term "Selling Stockholder" shall include the
Investor and any affiliate of such Investor;

                     (b) the term "Registration Statement" shall include
any final Prospectus, exhibit, supplement or amendment included in or relating
to the Registration Statement referred to in Section 7.1; and

                     (c) the term "untrue statement" shall include any
untrue statement or alleged untrue statement, or any omission or alleged
omission to state in the Registration Statement a material fact required to be
stated therein or necessary to make the statements therein, in the light of the
circumstances under which they were made, not misleading.

                                    (i) The Company agrees to indemnify and
hold harmless each Selling Stockholder from and against any losses, claims,
damages or liabilities to which such Selling Stockholder may become subject
(under the Securities Act or otherwise) insofar as such losses, claims,
damages or liabilities (or actions or proceedings in respect thereof) arise
out of, or are based upon (i) any untrue statement of a material fact
contained in the Registration Statement, or (ii) any failure by the Company
to fulfill any undertaking included in the Registration Statement, and the
Company will reimburse such Selling Stockholder for any reasonable legal or
other expenses reasonably incurred in investigating, defending or preparing
to defend any such action, proceeding or claim, provided, however, that 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, an untrue
statement made in such Registration Statement in reliance upon and in
conformity with written information furnished to the Company by or on behalf
of such Selling Stockholder specifically for use in preparation of the
Registration Statement or the failure of such Selling Stockholder to comply
with its covenants and agreements contained in Sections 5.1, 5.2, 5.3 or 7.2
hereof or any statement or omission in any Prospectus that is corrected in
any subsequent Prospectus that was delivered to the Investor prior to the
pertinent sale or sales by the Investor.

                                    (ii) The Investor agrees to indemnify and
hold harmless the Company (and each person, if any, who controls the Company
within the meaning of Section 15 of the Securities Act, each officer of the
Company who signs the Registration Statement and each director of the
Company) from and against any losses, claims, damages or liabilities to which
the Company (or any such officer, director or controlling person) may become
subject (under the Securities Act or otherwise), insofar as such losses,
claims, damages or liabilities (or actions or proceedings in respect thereof)
arise out of, or are based upon, (i) any failure to comply with the covenants
and agreements contained in Section 5.1, 5.2, 5.3 or 7.2 hereof, or (ii) any
untrue statement of a material fact contained in the Registration Statement
if such untrue statement was made in reliance upon and in conformity with
written information furnished by or on behalf of the Investor specifically
for use in preparation of the Registration Statement, and the Investor will
reimburse the Company (or such officer, director or controlling person), as
the case


                                       13
<PAGE>

may be, for any legal or other expenses reasonably incurred in investigating,
defending or preparing to defend any such action, proceeding or claim.

                                    (iii) Promptly after receipt by any
indemnified person of a notice of a claim or the beginning of any action in
respect of which indemnity is to be sought against an indemnifying person
pursuant to this Section 7.3, such indemnified person shall notify the
indemnifying person in writing of such claim or of the commencement of such
action, but the omission to so notify the indemnifying party will not relieve
it from any liability which it may have to any indemnified party under this
Section 7.3 (except to the extent that such omission materially and adversely
affects the indemnifying party's ability to defend such action) or from any
liability otherwise than under this Section 7.3. Subject to the provisions
hereinafter stated, in case any such action shall be brought against an
indemnified person, the indemnifying person shall be entitled to participate
therein, and, to the extent that it shall elect by written notice delivered
to the indemnified party promptly after receiving the aforesaid notice from
such indemnified party, shall be entitled to assume the defense thereof, with
counsel reasonably satisfactory to such indemnified person. After notice from
the indemnifying person to such indemnified person of its election to assume
the defense thereof, such indemnifying person shall not be liable to such
indemnified person for any legal expenses subsequently incurred by such
indemnified person in connection with the defense thereof, provided, however,
that if there exists or shall exist a conflict of interest that would make it
inappropriate, in the reasonable opinion of counsel to the indemnified
person, for the same counsel to represent both the indemnified person and
such indemnifying person or any affiliate or associate thereof, the
indemnified person shall be entitled to retain its own counsel at the expense
of such indemnifying person; provided, however, that no indemnifying person
shall be responsible for the fees and expenses of more than one separate
counsel (together with appropriate local counsel) for all indemnified
parties. In no event shall any indemnifying person be liable in respect of
any amounts paid in settlement of any action unless the indemnifying person
shall have approved the terms of such settlement; provided that such consent
shall not be unreasonably withheld. No indemnifying person shall, without the
prior written consent of the indemnified person, effect any settlement of any
pending or threatened proceeding in respect of which any indemnified person
is or could have been a party and indemnification could have been sought
hereunder by such indemnified person, unless such settlement includes an
unconditional release of such indemnified person from all liability on claims
that are the subject matter of such proceeding.

                                    (iv) If the indemnification provided for
in this Section 7.3 is unavailable to or insufficient to hold harmless an
indemnified party under subsection (a) or (b) above in respect of any losses,
claims, damages or liabilities (or actions or proceedings in respect thereof)
referred to therein, then each indemnifying party shall contribute to the
amount paid or payable by such indemnified party as a result of such losses,
claims, damages or liabilities (or actions in respect thereof) in such
proportion as is appropriate to reflect the relative fault of the Company on
the one hand and the Investors on the other in connection with the statements
or omissions or other matters which resulted in such losses, claims, damages
or liabilities (or actions in respect thereof), as well as any other relevant
equitable considerations. The relative fault shall be determined by reference
to, among other things, in the case of an untrue statement, whether the
untrue statement relates to information supplied by the Company on the one
hand or an Investor on the other and the parties' relative intent, knowledge,
access to information and opportunity to correct or prevent such untrue
statement. The Company and the Investors agree


                                       14
<PAGE>

that it would not be just and equitable if contribution pursuant to this
subsection (d) were determined by pro rata allocation (even if the Investors
were treated as one entity for such purpose) or by any other method of
allocation which does not take into account the equitable considerations
referred to above in this subsection (d). The amount paid or payable by an
indemnified party as a result of the losses, claims, damages or liabilities
(or actions in respect thereof) referred to above in this subsection (d)
shall be deemed to include any legal or other expenses reasonably incurred by
such indemnified party in connection with investigating or defending any such
action or claim. Notwithstanding the provisions of this subsection (d), no
Investor shall be required to contribute any amount in excess of the amount
by which the gross amount received by the Investor from the sale of the
Shares to which such loss relates exceeds the amount of any damages which
such Investor has otherwise been required to pay by reason of such untrue
statement. 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. The Investors' obligations in this subsection to
contribute are several in proportion to their sales of Shares to which such
loss relates and not joint.

                                    (v) The parties to this Agreement hereby
acknowledge that they are sophisticated business persons who were represented
by counsel during the negotiations regarding the provisions hereof including,
without limitation, the provisions of this Section 7.3, and are fully
informed regarding said provisions. They further acknowledge that the
provisions of this Section 7.3 fairly allocate the risks in light of the
ability of the parties to investigate the Company and its business in order
to assure that adequate disclosure is made in the Registration Statement as
required by the Act and the Exchange Act. The parties are advised that
federal or state public policy as interpreted by the courts in certain
jurisdictions may be contrary to certain of the provisions of this Section
7.3, and the parties hereto hereby expressly waive and relinquish any right
or ability to assert such public policy as a defense to a claim under this
Section 7.3 and further agree not to attempt to assert any such defense.

                  7.4 TERMINATION OF CONDITIONS AND OBLIGATIONS. The
conditions precedent imposed by Section 5 or this Section 7 upon the
transferability of the Shares shall cease and terminate as to any particular
number of the Shares when such Shares shall have been effectively registered
under the Securities Act and sold or otherwise disposed of in accordance with
the intended method of disposition set forth in the Registration Statement
covering such Shares or at such time as an opinion of counsel satisfactory to
the Company shall have been rendered to the effect that such conditions are
not necessary in order to comply with the Securities Act.

                  7.5 INFORMATION AVAILABLE. So long as the Registration
Statement is effective covering the resale of Shares owned by the Investor, the
Company will furnish to the Investor:

                     (a) as soon as practicable after it is available, one
copy of (i) its Annual Report to Stockholders (which Annual Report shall
contain financial statements audited in accordance with generally accepted
accounting principles by a national firm of certified public accountants) and
(ii) if not included in substance in the Annual Report to Stockholders, its
Annual Report on Form 10-K (the foregoing, in each case, excluding exhibits);



                                       15

<PAGE>

                     (b) upon the reasonable request of the Investor, all
exhibits excluded by the parenthetical to subparagraph (a)(ii) of this
Section 7.5 as filed with the SEC and all other information that is made
available to shareholders; and

                     (c) upon the reasonable request of the Investor, an
adequate number of copies of the Prospectuses to supply to any other party
requiring such Prospectuses; and the Company, upon the reasonable request of
the Investor, will meet with the Investor or a representative thereof at the
Company's headquarters to discuss all information relevant for disclosure in
the Registration Statement covering the Shares and will otherwise cooperate
with any Investor conducting an investigation for the purpose of reducing or
eliminating such Investor's exposure to liability under the Securities Act,
including the reasonable production of information at the Company's
headquarters; provided, that the Company shall not be required to disclose
any confidential information to or meet at its headquarters with any Investor
until and unless the Investor shall have entered into a confidentiality
agreement in form and substance reasonably satisfactory to the Company with
the Company with respect thereto.

                  7.6 The Company will not issue any public statement, press
release or any other public disclosure listing Investor as one of the
purchasers of the Shares without Investor's prior written consent.

         8. NOTICES. All notices, requests, consents and other communications
hereunder shall be in writing, shall be mailed (A) if within domestic United
States by first-class registered or certified airmail, or nationally
recognized overnight express courier, postage prepaid, or by facsimile, or
(B) if delivered from outside the United States, by International Federal
Express or facsimile, and shall be deemed given (i) if delivered by
first-class registered or certified mail domestic, three business days after
so mailed, (ii) if delivered by nationally recognized overnight carrier, one
(1) business day after so mailed, (iii) if delivered by International Federal
Express, two (2) business days after so mailed, (iv) if delivered by
facsimile, upon electric confirmation of receipt and shall be delivered as
addressed as follows:

                           (a) if to the Company, to:

                               Aurora Biosciences Corporation
                               11010 Torreyana Road
                               San Diego, California 92121

                               Attn:  Stuart J.M. Collinson
                               Chief Executive Officer
                               Phone:  (858) 404-6601
                               Telecopy:  (858) 404-6716



                                       16
<PAGE>

                           (b) with a copy mailed to:

                               Cooley Godward LLP
                               4365 Executive Drive
                               San Diego, CA  92121

                               Attn: Thomas A. Coll
                               Phone: (858) 550-6013
                               Telecopy: (858) 453-3555

                           (c) if to the Investor, at its address on the
Signature Page hereto, or at such other address or addresses as may have been
furnished to the Company in writing.

         9. CHANGES. This Agreement may not be modified or amended except
pursuant to an instrument in writing signed by the Company and the Investor.

         10. HEADINGS. The headings of the various sections of this Agreement
have been inserted for convenience of reference only and shall not be deemed to
be part of this Agreement.

         11. Severability. In case any provision contained in this Agreement
should be invalid, illegal or unenforceable in any respect, the validity,
legality and enforceability of the remaining provisions contained herein shall
not in any way be affected or impaired thereby.

         12. Governing Law. This Agreement shall be governed by, and construed
in accordance with, the internal laws of the State of California, without giving
effect to the principles of conflicts of law.

         13. Counterparts. This Agreement may be executed in two or more
counterparts, each of which shall constitute an original, but all of which, when
taken together, shall constitute but one instrument, and shall become effective
when one or more counterparts have been signed by each party hereto and
delivered to the other parties.

         14. CONFIDENTIAL DISCLOSURE AGREEMENT. Notwithstanding any provision of
this Agreement to the contrary, any confidential disclosure agreement previously
executed by the Company and the Investor in connection with the transactions
contemplated by this Agreement shall remain in full force and effect in
accordance with its terms following the execution of this Agreement and the
consummation of the transactions contemplated hereby.



                                       17
<PAGE>

<TABLE>
<CAPTION>
                                    EXHIBIT A

                         AURORA BIOSCIENCES CORPORATION

                         STOCK CERTIFICATE QUESTIONNAIRE


         Pursuant to Section 5 of the Agreement, please provide us with the
following information:
<S>       <C>                                       <C>
1.        The exact name that your Shares            __________________________
          are to be registered in (this is the
          name that will appear on your stock
          certificate(s)). You may use a
          nominee name if appropriate:

2.        The relationship between the Investor      __________________________
          and the registered holder listed
          in response to item 1 above:

3.        The mailing address of the registered      __________________________
          holder listed in response to
          item 1 above:

4.        The Social Security Number or Tax          __________________________
          Identification Number of the
          registered holder listed in the
          response to item 1 above:
</TABLE>






                                       A-1
<PAGE>



                                    EXHIBIT B

                         AURORA BIOSCIENCES CORPORATION

                             INVESTOR QUESTIONNAIRE

                (ALL INFORMATION WILL BE TREATED CONFIDENTIALLY)

To:  Aurora Biosciences Corporation

         This Investor Questionnaire ("Questionnaire") must be completed by
each potential investor in connection with the offer and sale of the shares
of the common stock, par value $0.001 per share, of Aurora Biosciences
Corporation (the "Securities"). The Securities are being offered and sold by
Aurora Biosciences Corporation (the "Corporation") without registration under
the Securities Act of 1933, as amended (the "Act"), and the securities laws
of certain states, in reliance on the exemptions contained in Section 4(2) of
the Act and on Regulation D promulgated thereunder and in reliance on similar
exemptions under applicable state laws. The Corporation must determine that a
potential investor meets certain suitability requirements before offering or
selling Securities to such investor. The purpose of this Questionnaire is to
assure the Corporation that each investor will meet the applicable
suitability requirements. The information supplied by you will be used in
determining whether you meet such criteria, and reliance upon the private
offering exemption from registration is based in part on the information
herein supplied.

         This Questionnaire does not constitute an offer to sell or a
solicitation of an offer to buy any security. Your answers will be kept
strictly confidential. However, by signing this Questionnaire you will be
authorizing the Corporation to provide a completed copy of this Questionnaire
to such parties as the Corporation deems appropriate in order to ensure that
the offer and sale of the Securities will not result in a violation of the
Act or the securities laws of any state and that you otherwise satisfy the
suitability standards applicable to purchasers of the Securities. All
potential investors must answer all applicable questions and complete, date
and sign this Questionnaire. Please print or type your responses and attach
additional sheets of paper if necessary to complete your answers to any item.

A.       BACKGROUND INFORMATION

Name:__________________________________________________________________________

Business Address:______________________________________________________________
                               (Number and Street)
_______________________________________________________________________________
(City)                         (State)                    (Zip Code)

Telephone Number:(   )_________________________________________________________

Residence Address:_____________________________________________________________
                               (Number and Street)

_______________________________________________________________________________
(City)                         (State)                    (Zip Code)

Telephone Number:  (   )_______________________________________________________

If an individual:

Age:______    Citizenship:______    Where registered to vote:__________________

If a corporation, partnership, limited liability company, trust or other entity:

Type of entity:________________________________________________________________

State of formation:______________  Date of formation:_________________________

Social Security or Taxpayer Identification No.________________________________

Send all correspondence to (check one):___Residence Address __Business Address



                                       B-1
<PAGE>

B.       STATUS AS ACCREDITED INVESTOR

The undersigned is an "accredited investor" as such term is defined in
Regulation D under the Act, as at the time of the sale of the Securities the
undersigned falls within one or more of the following categories (Please
initial one or more, as applicable):(1)

_____(1) a bank as defined in Section 3(a)(2) of the Act, or a savings and
loan association or other institution as defined in Section 3(a)(5)(A) of the
Act whether acting in its individual or fiduciary capacity; a broker or
dealer registered pursuant to Section 15 of the Securities Exchange Act of
1934; an insurance company as defined in Section 2(13) of the Act; an
investment company registered under the Investment Corporation Act of 1940 or
a business development company as defined in Section 2(a)(48) of that Act; a
Small Business Investment Corporation licensed by the U.S. Small Business
Administration under Section 301(c) or (d) of the Small Business Investment
Act of 1958; a plan established and maintained by a state, its political
subdivisions, or any agency or instrumentality of a state or its political
subdivisions for the benefit of its employees, if such plan has total assets
in excess of $5,000,000; an employee benefit plan within the meaning of the
Employee Retirement Income Security Act of 1974 if the investment decision is
made by a plan fiduciary, as defined in Section 3(21) of such Act, which is
either a bank, savings and loan association, insurance company, or registered
investment adviser, or if the employee benefit plan has total assets in
excess of $5,000,000 or, if a self-directed plan, with the investment
decisions made solely by persons that are accredited investors;1

_____(2) a private business development company as defined in Section
202(a)(22) of the Investment Adviser Act of 1940;

_____(3) an organization described in Section 501(c)(3) of the Internal
Revenue Code of 1986, as amended, corporation, Massachusetts or similar
business trust, or partnership, not formed for the specific purpose of
acquiring the Securities offered, with total assets in excess of $5,000,000;

_____(4) a natural person whose individual net worth, or joint net worth with
that person's spouse, at the time of such person's purchase of the Securities
exceeds $1,000,000;

_____(5) a natural person who had an individual income in excess of $200,000
in each of the two most recent years or joint income with that person's
spouse in excess of $300,000 in each of those years and has a reasonable
expectation of reaching the same income level in the current year;

_____(6) a trust, with total assets in excess of $5,000,000, not formed for
the specific purpose of acquiring the Securities offered, whose purchase is
directed by a sophisticated person as described in Rule 506(b)(2)(ii) of
Regulation D; and

_____(7) an entity in which all of the equity owners are accredited investors
(as defined above).

-------------------------------------------------------------------------------
1 As used in this Questionnaire, the term "net worth" means the excess of total
assets over total liabilities. In computing net worth for the purpose of
subsection (4), the principal residence of the investor must be valued at cost,
including cost of improvements, or at recently appraised value by an
institutional lender making a secured loan, net of encumbrances. In determining
income, the investor should add to the investor's adjusted gross income any
amounts attributable to tax exempt income received, losses claimed as a limited
partner in any limited partnership, deductions claimed for depiction,
contributions to an IRA or KEOGH retirement plan, alimony payments, and any
amount by which income from long-term capital gains has been reduced in arriving
at adjusted gross income.



                                       B-2
<PAGE>


C.       REPRESENTATIONS

The undersigned hereby represents and warrants to the Corporation as follows:

         1. Any purchase of the Securities would be solely for the account of
the undersigned and not for the account of any other person or with a view to
any resale, fractionalization, division, or distribution thereof.

         2. The information contained herein is complete and accurate and may
be relied upon by the Corporation, and the undersigned will notify the
Corporation immediately of any material change in any of such information
occurring prior to the closing, if any, with respect to the purchase of
Securities by the undersigned or any co-purchaser.

         3. There are no suits, pending litigation, or claims against the
undersigned that could materially affect the net worth of the undersigned as
reported in this Questionnaire.

         4. The undersigned acknowledges that there may occasionally be times
when the Corporation, based on the advice of its counsel, determines that it
must suspend the use of the Prospectus forming a part of the Registration
Statement (as such terms are defined in the Stock Purchase Agreement to which
this Questionnaire is attached) until such time as an amendment to the
Registration Statement has been filed by the Company and declared effective by
the Securities and Exchange Commission or until the Corporation has amended or
supplemented such Prospectus. The undersigned is aware that, in such event, the
Securities will not be subject to ready liquidation, and that any Securities
purchased by the undersigned would have to be held during such suspension. The
overall commitment of the undersigned to investments which are not readily
marketable is not excessive in view of the undersigned's net worth and financial
circumstances, and any purchase of the Securities will not cause such commitment
to become excessive. The undersigned is able to bear the economic risk of an
investment in the Securities.

         5. In addition to reviewing the Corporation's Confidential Offering
Memorandum, the undersigned has carefully considered the potential risks
relating to the Corporation and a purchase of the Securities, and fully
understands that the Securities are speculative investments which involve a
high degree of risk of loss of the undersigned's entire investment. Among
others, the undersigned has carefully considered each of the risks described
under the heading "Risk Factors" in the Corporation's most recent annual
report on Form 10-K.

IN WITNESS WHEREOF, the undersigned has executed this Questionnaire this _____
day of _____________, 2000, and declares under oath that it is truthful and
correct.



                                 Print Name____________________________________

                                 By:___________________________________________
                                 Signature

                                 Title:________________________________________
                                       (required for any purchaser that is a
                                       corporation, partnership, trust or other
                                       entity)






                                       B-3
<PAGE>



                                    EXHIBIT C

                         AURORA BIOSCIENCES CORPORATION

                         CERTIFICATE OF SUBSEQUENT SALE

ChaseMellon Shareholder Services

         RE:      Sale of Shares of Common Stock of Aurora Biosciences
                  Corporation (the "Company") pursuant to the Company's
                  Prospectus dated _______________, 2000 (the "Prospectus")

Dear Sir/Madam:

         The undersigned hereby certifies, in connection with the sale of shares
of Common Stock of the Company included in the table of Selling Shareholders in
the Prospectus, that the undersigned has sold the Shares pursuant to the
Prospectus and in a manner described under the caption "Plan of Distribution" in
the Prospectus and that such sale complies with all applicable securities laws,
including, without limitation, the Prospectus delivery requirements of the
Securities Act of 1933, as amended.

         Selling Shareholder (the beneficial owner):___________________________

         Record Holder (e.g., if held in name of nominee):_____________________

         Restricted Stock Certificate No.(s):__________________________________

         Number of Shares Sold:________________________________________________

         Date of Sale:_________________________________________________________

         In the event that you receive a stock certificate(s) representing more
shares of Common Stock than have been sold by the undersigned, then you should
return to the undersigned a newly issued certificate for such excess shares in
the name of the Record Holder and BEARING A RESTRICTIVE LEGEND. Further, you
should place a stop transfer on your records with regard to such certificate.

                                                   Very truly yours,

                                                   By:_________________________

                                                   Print Name:_________________

                                                   Title:______________________

Dated:_____________________________

cc:      Investor Relations
         Aurora Biosciences Corporation
         11010 Torreyana Road
         San Diego, California  92121



                                       C-1
<PAGE>
<TABLE>
<CAPTION>
                                   SCHEDULE A
                                LIST OF INVESTORS
<S>                                                                        <C>                   <C>
                                                                                                   AGGREGATE
NAME AND ADDRESS                                                           SHARES                PURCHASE PRICE
---------------------------------------------------------------------   -------------     ---------------------
JANUS INVESTMENT FUND
BY: BOUYBREESE & CO.                                                       919,050                $38,600,100


JANUS INVESTMENT FUND
BY: BOOKBEND & CO.                                                         380,950                $15,999,900


BLACKROCK FUNDS
BY: BARNETT AND CO.                                                        400,000                $16,800,000


TISCH FINANCIAL MANAGEMENT
BY: BAKER BROS. INVESTMENTS, LLC                                            50,000                $ 2,100,000


TISCH FINANCIAL MANAGEMENT
BY: FOUR PARTNERS                                                           50,000                $ 2,100,000


TOTAL                                                                    1,800,000                $75,600,000
</TABLE>