<PAGE>   1

                                                                   EXHIBIT 10.66

                    AMENDMENT TO SEVERANCE BENEFITS AGREEMENT

        This AMENDMENT (the "Amendment") to the Severance Benefits Agreement
(the "Agreement") dated February 6, 1998 by and between CYTEL CORPORATION (the
"Company"), and VIRGIL THOMPSON ("Employee") and attached hereto as Exhibit A,
is entered into as of June 2, 1999 (the "Amendment Date").

                                    RECITALS

        WHEREAS, the parties hereto desire to amend the Agreement in the manner
set forth in this Amendment in order to provide severance benefits to the
Employee as reflected in this Amendment.

                                    AGREEMENT

        NOW, THEREFORE, in consideration of the benefits described below and the
mutual promises hereinafter set forth, the parties hereto agree as follows:

1.      Capitalized terms used but not otherwise defined in this Amendment shall
        have the meanings given such terms in the Agreement.

2.      The two indented paragraphs on the top of page 3 of the Agreement (as
        noted on page 3 of Exhibit A) are hereby amended and restated in their
        entirety as follows:

                (1)     SEVERANCE BENEFIT: On June 3, 1999 ("Severance Date"),
                you will be entitled to a severance benefit to be paid in the
                form and manner set forth in this Section (1) equivalent to six
                (6) months Base Salary ("Severance Benefit"). On the Severance
                Date, you will be issued a warrant in the form attached hereto
                as Exhibit B, to purchase a number of shares of Common Stock in
                the Company with a value equivalent to the value of your
                Severance Benefit plus forty percent (40%) ($220,500). The value
                of the Common Stock and the exercise price of the warrant shall
                be equal to the closing price of the Company's Common Stock on
                the Nasdaq National Market on the Severance Date.

                The exercise date of the warrant issued pursuant to this Section
                (1) will be four (4) years from the date it is issued. The
                warrant shall be fully vested and will include a net exercise
                provision.

                (2)     SUCCESS BONUS: You will be eligible to receive a success
                bonus ("Success Bonus") on the closing date of the merger
                ("Closing Date") and on December 31, 1999 under the
                circumstances provided in this Section (2).

                You will be entitled to a Success Bonus on the Closing Date if
                the Company's cash or similar assets exceed liabilities on the
                Closing Date by more than $315,000 ("Excess Cash Value") as
                reflected in the Company's financial statements. If Excess Cash
                Value exists, you will receive a Success Bonus of five (5)% of
                the Excess Cash Value.



                                       1.
<PAGE>   2

                You will be entitled to an additional Success Bonus if the
                Company's proceeds (net of any out-of-pocket expenses incurred
                in order to realize those proceeds) from the sale of
                non-Epimmune assets prior to December 31, 1999, aggregated with
                the Company's other assets as reflected on the Company's
                financial statements on the Closing Date, exceed the Company's
                liabilities by more than $315,000 as of the Closing Date (Year
                End Excess Cash Value). If Year End Excess Cash Value exists,
                you will be entitled to a Success Bonus equivalent to 5% of the
                amount by which the Year End Excess Cash Value exceeds the
                Excess Cash Value.

                The Company agrees to prepare and provide to you a statement
                reflecting whether there is any Excess Cash Value and/or Year
                End Excess Cash Value and the amount of your Success Bonus, if
                any, within fifteen (15) days of the Closing Date and by January
                15, 1999. Within 15 days of notice from the Company that you are
                entitled to a Success Bonus, you agree to notify Company in
                writing of the format in which you elect to receive the Success
                Bonus. You may elect to receive the cash value of the Success
                Bonus or to accept the Success Bonus in the form of a warrant to
                purchase a number of shares of Common Stock in the Company with
                a value equivalent to the cash value to which you are entitled.
                The value of the Common Stock and the exercise price of the
                warrant will be equal to the closing price of the Company's
                Common Stock on the Nasdaq National Market on the Separation
                Date.

                If you elect to receive a Success Bonus, if any, issued in the
                form of a warrant, you will have 4 years from the date the
                warrant is issued to exercise the warrant. The warrant shall be
                fully vested and shall include a net exercise provision; and

                (3)     CURRENT STOCK OPTIONS: Each of the stock options you
                currently hold to purchase Common Stock of the Company
                ("Options") shall: (i) be accelerated such that the number of
                vested shares under the Options shall equal 56,408 shares, and
                (ii) be exercisable up to and including four (4) years from the
                Severance Date.

3.      Except as specifically amended by this Amendment and the Attachments
        hereto, the terms and conditions of the Agreement shall remain in full
        force and effect.

4.      This Amendment and the Attachments hereto, shall be governed by and
        construed in accordance with the laws of the State of California,
        without regard to its choice of law provisions.

5.      This Amendment may be executed in two or more counterparts, each of
        which shall be deemed an original, but all of which together shall
        constitute one and the same instrument.

6.      This Amendment and the Attachments hereto, constitute the entire
        agreement between Employee and the Company. It is entered into without
        reliance on any promise or representation other than those expressly
        contained in this Amendment and the Attachments hereto.



                                       2.
<PAGE>   3

        IN WITNESS WHEREOF, the parties have executed this Amendment on the day
and year first written above.

        CYTEL CORPORATION

By: /s/ Howard E. Greene                /s/ Virgil Thompson
   ----------------------------------   ----------------------------------------
   HOWARD E. GREENE, JR.                VIRGIL THOMPSON
   CHAIRMAN OF THE BOARD



                                       3.
<PAGE>   4

THE SECURITIES REPRESENTED BY THIS CERTIFICATE HAVE BEEN ACQUIRED FOR INVESTMENT
AND HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933 OR ANY STATE
SECURITIES LAWS. SUCH SECURITIES MAY NOT BE SOLD OR TRANSFERRED IN THE ABSENCE
OF SUCH REGISTRATION OR AN EXEMPTION THEREFROM UNDER SAID ACT AND ANY APPLICABLE
STATE SECURITIES LAWS.

                           WARRANT TO PURCHASE SHARES
                               OF COMMON STOCK OF
                                CYTEL CORPORATION
                            (VOID AFTER JUNE 2, 2003)

        This certifies that VIRGIL THOMPSON or assigns (the "Holder"), for value
received, is entitled to purchase from CYTEL CORPORATION, a Delaware corporation
(the "Company"), having a place of business at 9393 Towne Centre Drive, San
Diego, California 92121, a maximum of [117,600] fully paid and nonassessable
shares of the Company's Common Stock ("Common Stock") for cash at a price of
$1.875 per share (the "Stock Purchase Price") at any time or from time to time
up to and including 5:00 p.m. (Pacific time) on June 2, 2003 (the "Expiration
Date"), upon surrender to the Company at its principal office (or at such other
location as the Company may advise the Holder in writing) of this Warrant
properly endorsed with the Form of Subscription attached hereto duly filled in
and signed and, if applicable, upon payment in cash or by check of the aggregate
Stock Purchase Price for the number of shares for which this Warrant is being
exercised determined in accordance with the provisions hereof. The Stock
Purchase Price and the number of shares purchasable hereunder are subject to
adjustment as provided in Section 3 of this Warrant.

        This Warrant is subject to the following terms and conditions:



                                       1.
<PAGE>   5

1.      EXERCISE; ISSUANCE OF CERTIFICATES; PAYMENT FOR SHARES.

                1.1     GENERAL. This Warrant is exercisable at the option of
the holder of record hereof, at any time or from time to time, up to the
Expiration Date for all or any part of the shares of Common Stock (but not for a
fraction of a share) which may be purchased hereunder. The Company agrees that
the shares of Common Stock purchased under this Warrant shall be and are deemed
to be issued to the Holder hereof as the record owner of such shares as of the
close of business on the date on which this Warrant shall have been surrendered,
properly endorsed, the completed, executed Form of Subscription delivered and
payment made for such shares. Certificates for the shares of Common Stock so
purchased, together with any other securities or property to which the Holder
hereof is entitled upon such exercise, shall be delivered to the Holder hereof
by the Company at the Company's expense within a reasonable time after the
rights represented by this Warrant have been so exercised. In case of a purchase
of less than all the shares which may be purchased under this Warrant, the
Company shall cancel this Warrant and execute and deliver a new Warrant or
Warrants of like tenor for the balance of the shares purchasable under the
Warrant surrendered upon such purchase to the Holder hereof within a reasonable
time. Each stock certificate so delivered shall be in such denominations of
Common Stock as may be requested by the Holder hereof and shall be registered in
the name of such Holder.

                1.2     NET ISSUE EXERCISE. Notwithstanding any provisions
herein to the contrary, if the fair market value of one share of the Company's
Common Stock is greater than the Stock Purchase Price (at the date of
calculation as set forth below), in lieu of exercising this Warrant for cash,
the Holder may elect to receive shares equal to the value (as determined below)
of this Warrant (or the portion thereof being canceled) by surrender of this
Warrant at the principal office of the Company together with the properly
endorsed Form of Subscription and notice of such election in which event the
Company shall issue to the Holder a number of shares of Common Stock computed
using the following formula:

                      X = Y (A-B)
                            -----
                              A

                Where X  = the number of shares of Common Stock to be issued to
                           the Holder

                Y    =     the number of shares of Common Stock purchasable
                           under the Warrant or, if only a portion of the
                           Warrant is being exercised, the portion of the
                           Warrant being canceled (at the date of such
                           calculation)

                A    =     the fair market value of one share of the Company's
                           Common Stock (at the date of such calculation)

                B    =     Stock Purchase Price (as adjusted to the date of such
                           calculation)



                                       2.
<PAGE>   6

For purposes of the above calculation, if the Company's Common Stock is then
traded on a securities exchange or through the Nasdaq National Market, the fair
market value of one share of Common Stock shall be deemed to be the average of
the closing sales prices for one share of Common Stock on such exchange for the
ten (10) trading days immediately preceding the date of exercise, and otherwise
the fair market value of one share of Common Stock shall be determined by the
Company's Board of Directors in good faith.

        2.      SHARES TO BE FULLY PAID; RESERVATION OF SHARES. The Company
covenants and agrees that all shares of Common Stock which may be issued upon
the exercise of the rights represented by this Warrant will, upon issuance, be
duly authorized, validly issued, fully paid and nonassessable and free from all
preemptive rights of any stockholder and free of all taxes, liens and charges
with respect to the issue thereof. The Company further covenants and agrees
that, during the period within which the rights represented by this Warrant may
be exercised, the Company will at all times have authorized and reserved, for
the purpose of issue or transfer upon exercise of the subscription rights
evidenced by this Warrant, a sufficient number of shares of authorized but
unissued Common Stock, or other securities and property, when and as required to
provide for the exercise of the rights represented by this Warrant. The Company
will take all such action as may be necessary to assure that such shares of
Common Stock may be issued as provided herein without violation of any
applicable law or regulation, or of any requirements of any domestic securities
exchange upon which the Common Stock may be listed; provided, however, that the
Company shall not be required to effect a registration under Federal or State
securities laws with respect to such exercise. The Company will not take any
action which would result in any adjustment of the Stock Purchase Price (as set
forth in Section 3 hereof) if the total number of shares of Common Stock
issuable after such action upon exercise of all outstanding warrants, together
with all shares of Common Stock then outstanding and all shares of Common Stock
then issuable upon exercise of all options and upon the conversion of all
convertible securities then outstanding, would exceed the total number of shares
of Common Stock then authorized by the Company's Certificate of Incorporation.

        3.      ADJUSTMENT OF STOCK PURCHASE PRICE AND NUMBER OF SHARES. The
Stock Purchase Price and the number of shares purchasable upon the exercise of
this Warrant shall be subject to adjustment from time to time upon the
occurrence of certain events described in this Section 3. Upon each adjustment
of the Stock Purchase Price, the Holder of this Warrant shall thereafter be
entitled to purchase, at the Stock Purchase Price resulting from such
adjustment, the number of shares obtained by multiplying the Stock Purchase
Price in effect immediately prior to such adjustment by the number of shares
purchasable pursuant hereto immediately prior to such adjustment, and dividing
the product thereof by the Stock Purchase Price resulting from such adjustment.

                3.1     SUBDIVISION OR COMBINATION OF STOCK. In case the Company
shall at any time subdivide its outstanding shares of Common Stock into a
greater number of shares, the Stock Purchase Price in effect immediately prior
to such subdivision shall be proportionately reduced, and conversely, in case
the outstanding shares of Common Stock of the Company shall be combined into a
smaller number of shares, the Stock Purchase Price in effect immediately prior
to such combination shall be proportionately increased.



                                       3.
<PAGE>   7

                3.2     DIVIDENDS IN COMMON STOCK, OTHER STOCK, PROPERTY,
RECLASSIFICATION. If at any time or from time to time the Holder of Common Stock
(or any shares of stock or other securities at the time receivable upon the
exercise of this Warrant) shall have received or become entitled to receive,
without payment therefor,

                        (a)     Common Stock or any shares of stock or other
securities which are at any time directly or indirectly convertible into or
exchangeable for Common Stock, or any rights or options to subscribe for,
purchase or otherwise acquire any of the foregoing by way of dividend or other
distribution,

                        (b)     any cash paid or payable otherwise than as a
cash dividend, or

                        (c)     Common Stock or additional stock or other
securities or property (including cash) by way of spinoff, split-up,
reclassification, combination of shares or similar corporate rearrangement,
(other than shares of Common Stock issued as a stock split or adjustments in
respect of which shall be covered by the terms of Section 3.1 above), then and
in each such case, the Holder shall, upon the exercise of this Warrant, be
entitled to receive, in addition to the number of shares of Common Stock
receivable thereupon, and without payment of any additional consideration
therefor, the amount of stock and other securities and property (including cash
in the cases referred to in clause (b) above and this clause (c)) which the
Holder would hold on the date of such exercise had he been the holder of record
of such Common Stock as of the date on which the holder of Common Stock received
or became entitled to receive such shares or all other additional stock and
other securities and property.

                3.3     REORGANIZATION, RECLASSIFICATION, CONSOLIDATION, MERGER
OR SALE. If any recapitalization, reclassification or reorganization of the
capital stock of the Company, or any consolidation or merger of the Company with
another corporation, or the sale of all or substantially all of its assets or
other transaction shall be effected in such a way that holders of Common Stock
shall be entitled to receive stock, securities, or other assets or property (an
"Organic Change"), then, as a condition of such Organic Change, lawful and
adequate provisions shall be made by the Company whereby the Holder shall
thereafter have the right to purchase and receive (in lieu of the shares of the
Common Stock of the Company immediately theretofore purchasable and receivable
upon the exercise of the rights represented hereby) such shares of stock,
securities or other assets or property as may be issued or payable with respect
to or in exchange for a number of outstanding shares of such Common Stock equal
to the number of shares of such stock immediately theretofore purchasable and
receivable upon the exercise of the rights represented hereby; provided,
however, that in the event the value of the stock, securities or other assets or
property (determined in good faith by the Board of Directors of the Company)
issuable or payable with respect to one share of the Common Stock of the Company
immediately theretofore purchasable and receivable upon the exercise of the
rights represented hereby is in excess of the Stock Purchase Price hereof
effective at the time of a merger and securities received in such
reorganization, if any, are publicly traded, then this Warrant shall expire
unless exercised prior to such Organic Change. In the event of any Organic
Change, appropriate provision shall be made by the Company with respect to the
rights and interests of the Holder of this Warrant to the end that the
provisions hereof (including, without limitation, provisions for adjustments of
the Stock Purchase Price and of the number of shares purchasable and receivable
upon the exercise of



                                       4.
<PAGE>   8

this Warrant) shall thereafter be applicable, in relation to any shares of
stock, securities or assets thereafter deliverable upon the exercise hereof. The
Company will not effect any such consolidation, merger or sale unless, prior to
the consummation thereof, the successor corporation (if other than the Company)
resulting from such consolidation or the corporation purchasing such assets
shall assume by written instrument reasonably satisfactory in form and substance
to the Holder substantially similar to the Warrant to purchase Common Stock,
executed and mailed or delivered to the registered Holder hereof at the last
address of such Holder appearing on the books of the Company, the obligation to
deliver to such Holder such shares of stock, securities or assets as, in
accordance with the foregoing provisions, such Holder may be entitled to
purchase.

                3.4     CERTAIN EVENTS. If any change in the outstanding Common
Stock of the Company or any other event occurs as to which the other provisions
of this Section 3 are not strictly applicable or if strict application would not
fairly protect the purchase rights of the Holder of the Warrant in accordance
with such provisions, then the Board of Directors of the Company shall make an
adjustment in the number and class of shares available under the Warrant, the
Stock Purchase Price or the application of such provisions, so as to protect
such purchase rights as aforesaid. The adjustment shall be such as will give the
Holder of the Warrant upon exercise for the same aggregate Stock Purchase Price
the total number, class and kind of shares as he would have owned had the
Warrant been exercised prior to the event and had he continued to hold such
shares until after the event requiring adjustment. 3.5 NOTICES OF CHANGE.

                        (a)     Immediately upon any adjustment in the number or
class of shares subject to this Warrant and of the Stock Purchase Price, the
Company shall give written notice thereof to the Holder, setting forth in
reasonable detail and certifying the calculation of such adjustment.

                        (b)     The Company shall give written notice to the
Holder at least 10 business days prior to the date on which the Company closes
its books or takes a record for determining rights to receive any dividends or
distributions.

                        (c)     The Company shall also give written notice to
the Holder at least 30 business days prior to the date on which an Organic
Change shall take place.

        4.      ISSUE TAX. The issuance of certificates for shares of Common
Stock upon the exercise of the Warrant shall be made without charge to the
Holder of the Warrant for any issue tax (other than any applicable income taxes)
in respect thereof; provided, however, that the Company shall not be required to
pay any tax which may be payable in respect of any transfer involved in the
issuance and delivery of any certificate in a name other than that of the then
Holder of the Warrant being exercised.

        5.      CLOSING OF BOOKS. The Company will at no time close its transfer
books against the transfer of any warrant or of any shares of Common Stock
issued or issuable upon the exercise of any warrant in any manner which
interferes with the timely exercise of this Warrant.



                                       5.
<PAGE>   9

        6.      NO VOTING OR DIVIDEND RIGHTS; LIMITATION OF LIABILITY. Nothing
contained in this Warrant shall be construed as conferring upon the Holder
hereof the right to vote or to consent or to receive notice as a shareholder of
the Company or any other matters or any rights whatsoever as a shareholder of
the Company. No dividends or interest shall be payable or accrued in respect of
this Warrant or the interest represented hereby or the shares purchasable
hereunder until, and only to the extent that, this Warrant shall have been
exercised. No provisions hereof, in the absence of affirmative action by the
holder to purchase shares of Common Stock, and no mere enumeration herein of the
rights or privileges of the holder hereof, shall give rise to any liability of
such Holder for the Stock Purchase Price or as a stockholder of the Company,
whether such liability is asserted by the Company or by its creditors.

        7.      WARRANTS TRANSFERABLE. Subject to compliance with applicable
federal and state securities laws, this Warrant and all rights hereunder are
transferable, in whole or in part, without charge to the holder hereof (except
for transfer taxes), upon surrender of this Warrant properly endorsed. Each
taker and holder of this Warrant, by taking or holding the same, consents and
agrees that this Warrant, when endorsed in blank, shall be deemed negotiable,
and that the holder hereof, when this Warrant shall have been so endorsed, may
be treated by the Company, at the Company's option, and all other persons
dealing with this Warrant as the absolute owner hereof for any purpose and as
the person entitled to exercise the rights represented by this Warrant, or to
the transfer hereof on the books of the Company any notice to the contrary
notwithstanding; but until such transfer on such books, the Company may treat
the registered owner hereof as the owner for all purposes.

        8.      RIGHTS AND OBLIGATIONS SURVIVE EXERCISE OF WARRANT. The rights
and obligations of the Company, of the holder of this Warrant and of the holder
of shares of Common Stock issued upon exercise of this Warrant, shall survive
the exercise of this Warrant.

        9.      INVESTMENT REPRESENTATIONS.

                9.1     PURCHASE FOR OWN ACCOUNT. Holder represents that it is
acquiring this Warrant and the Common Stock issuable upon exercise of this
Warrant (collectively, the "Securities") solely for its own account and
beneficial interest for investment and not for sale or with a view to
distribution of the Securities or any part thereof, has no present intention of
selling (in connection with a distribution or otherwise), granting any
participation in, or otherwise distributing the same, and does not presently
have reason to anticipate a change in such intention.

                9.2     INFORMATION AND SOPHISTICATION. Holder acknowledges that
it has received all the information it has requested from the Company and
considers necessary or appropriate for deciding whether to acquire this Warrant.
Holder represents that it has had an opportunity to ask questions and receive
answers from the Company regarding the terms and conditions of the offering of
this Warrant and to obtain any additional information necessary to verify the
accuracy of the information given the Holder. Holder further represents that it
has such knowledge and experience in financial and business matters that it is
capable of evaluating the merits and risk of this investment.



                                       6.
<PAGE>   10

                9.3     ABILITY TO BEAR ECONOMIC RISK. Holder acknowledges that
investment in this Warrant involves a high degree of risk, and represents that
it is able, without materially impairing its financial condition, to hold the
Securities for an indefinite period of time and to suffer a complete loss of its
investment.

                9.4     FURTHER LIMITATIONS ON DISPOSITION. Without in any way
limiting the representations set forth above, Holder further agrees not to make
any disposition of all or any portion of the Securities unless and until:

                        (a)     There is then in effect a Registration Statement
under the Securities Act of 1933, as amended (the "1933 Act"), covering such
proposed disposition and such disposition is made in accordance with such
Registration Statement; or

                        (b)     (i) Holder shall have notified the Company of
the proposed disposition and shall have furnished the Company with a detailed
statement of the circumstances surrounding the proposed disposition, and (ii) if
reasonably requested by the Company, Holder shall have furnished the Company
with an opinion of counsel, reasonably satisfactory to the Company, that such
disposition will not require registration under the 1933 Act.

                Notwithstanding the provisions of paragraphs (a) and (b) above,
no such registration statement or opinion of counsel shall be necessary for a
transfer by Holder to a stockholder or partner (or retired partner) of such
Holder, or transfers by gift, will or intestate succession to any spouse or
lineal descendants or ancestors, if all transferees agree in writing to be
subject to the terms hereof to the same extent as if they were a Holder
hereunder.

        10.     MODIFICATION AND WAIVER. This Warrant and any provision hereof
may be changed, waived, discharged or terminated only by an instrument in
writing signed by the party against which enforcement of the same is sought.

        11.     NOTICES. Any notice, request or other document required or
permitted to be given or delivered to the holder hereof or the Company shall be
delivered or shall be sent by certified mail, postage prepaid, to each such
holder at its address as shown on the books of the Company or to the Company at
the address indicated therefor in the first paragraph of this Warrant or such
other address as either may from time to time provide to the other.

        12.     BINDING EFFECT ON SUCCESSORS. This Warrant shall be binding upon
any corporation succeeding the Company by merger, consolidation or acquisition
of all or substantially all of the Company's assets. All of the obligations of
the Company relating to the Common Stock issuable upon the exercise of this
Warrant shall survive the exercise and termination of this Warrant. All of the
covenants and agreements of the Company shall inure to the benefit of the
successors and assigns of the holder hereof.

        13.     DESCRIPTIVE HEADINGS AND GOVERNING LAW. The description headings
of the several sections and paragraphs of this Warrant are inserted for
convenience only and do not constitute a part of this Warrant. This Warrant
shall be construed and enforced in accordance with, and the rights of the
parties shall be governed by, the laws of the State of California.



                                       7.
<PAGE>   11

        14.     LOST WARRANTS. The Company represents and warrants to the Holder
hereof that upon receipt of evidence reasonably satisfactory to the Company of
the loss, theft, destruction, or mutilation of this Warrant and, in the case of
any such loss, theft or destruction, upon receipt of an indemnity reasonably
satisfactory to the Company, or in the case of any such mutilation upon
surrender and cancellation of such Warrant, the Company, at its expense, will
make and deliver a new Warrant, of like tenor, in lieu of the lost, stolen,
destroyed or mutilated Warrant.

        15.     FRACTIONAL SHARES. No fractional shares shall be issued upon
exercise of this Warrant. The Company shall, in lieu of issuing any fractional
share, pay the holder entitled to such fraction a sum in cash equal to such
fraction multiplied by the then effective Stock Purchase Price.



                      [THIS SPACE INTENTIONALLY LEFT BLANK]



                                       8.
<PAGE>   12

        IN WITNESS WHEREOF, the Company has caused this Warrant to be duly
executed by its officers, thereunto duly authorized this 3rd day of June, 1999.


                                        CYTEL CORPORATION

                                        By:
                                           -------------------------------------

                                        Title:
                                              ----------------------------------


ATTEST:


-------------------------------------
Secretary



<PAGE>   13

                                    EXHIBIT A

                                SUBSCRIPTION FORM

                                                         Date: _________________

Cytel Corporation
9393 Towne Centre Drive
San Diego, CA 92121

Attn:  Secretary

Ladies and Gentlemen:

[ ]     The undersigned hereby elects to exercise the warrant issued to it by
        Cytel Corporation (the "Company") and dated June __, 1999 (the
        "Warrant") and to purchase thereunder __________________________________
        shares of the Common Stock of the Company (the "Shares") at a purchase
        price of ___________________________________________ Dollars
        ($__________) per Share or an aggregate purchase price of
        __________________________________ Dollars ($__________) (the "Purchase
        Price").

[ ]     The undersigned hereby elects to convert _______________________ percent
        (____%) of the value of the Warrant pursuant to the provisions of
        Section 1.2 of the Warrant.

        Pursuant to the terms of the Warrant the undersigned has delivered the
Purchase Price herewith in full in cash or by certified check or wire transfer.


                                        Very truly yours,

                                        ----------------------------------------
                                        Signature

                                        ----------------------------------------
                                        Printed Name