<PAGE>


                                                                    EXHIBIT 4.4

                                AMENDMENT TO THE
                 PREFERRED STOCK AND WARRANT PURCHASE AGREEMENT

         This Amendment (the "AMENDMENT") to that certain Preferred Stock and
Warrant Purchase Agreement (the "AGREEMENT") dated as of February 5, 2003 and
amended as of February 11, 2003, between INTRABIOTICS PHARMACEUTICALS, INC., a
Delaware corporation (the "Company"), and the undersigned (the "INVESTOR"), is
made and entered into as of April 10, 2003, by and between the Company and the
Investor. Capitalized terms used herein without definition shall have the
meanings assigned to such terms in the Agreement.

1.       Section 3.1 of Annex I to the Agreement is amended to read in its
entirety as follows:

                  "3.1 The completion of the purchase and sale of the Shares and
         the Warrants (the "Closing") shall occur on the date which is at least
         ten (10) days after the condition set forth in Section 3.3(e) shall
         have been satisfied; provided that all other conditions set forth in
         this Section 3 also shall have been satisfied, or if the condition set
         forth in Section 3.3(e) is not required to be satisfied, then the tenth
         (10th) business day after the date of a meeting of the Company's
         stockholders at which the approval of the Offering was solicited in
         accordance with the Nasdaq Rules, or on such other date as the Company
         and the Investors may mutually agree (the "Closing Date"). At the
         Closing, the aggregate purchase price for the Shares shall be delivered
         to the Company pursuant to the escrow instructions attached hereto as
         EXHIBIT G (the "Escrow Instructions"). As soon as reasonably practical,
         but in no event later than five (5) business days, after the Closing,
         the Company shall deliver to the Investor, versus payment therefor, one
         or more stock certificates representing the number of Shares set forth
         on the Signature Page hereto and one or more Warrants to purchase the
         number of shares of Common Stock set forth on the Signature Page
         hereto, each such certificate and Warrant to be registered in the name
         of the Investor or, if so indicated on the Stock Certificate and
         Warrant Questionnaire attached hereto as EXHIBIT D, in the name of a
         nominee designated by the Investor."

2.       Sections 3.3(g) of Annex I to the Agreement is amended to read in its
entirety as follows:

                  "(G) No proceeding challenging this Agreement, the Offering or
         the transactions contemplated by the Agreements, or seeking to
         prohibit, alter, prevent or delay the Closing shall have been
         instituted by any federal, state or local government, or any
         administrative agency or commission or other governmental authority or
         agency, domestic or foreign."

3.       Annex I to the Agreement is hereby amended to add new Section 18, which
shall read in its entirety as follows:

                  "18. ESCROW. No later than 2:00 p.m. New York time on
         Thursday, April 10, 2003 the Investor shall deposit $_________ into an
         Escrow Account at Cooley Godward LLP pursuant to the terms of the
         Escrow Instructions."
<PAGE>
         4. Section 4.c. of the Certificate of Designation attached as Exhibit A
to the Agreement is hereby amended to read in its entirety as follows:

                  "c. Conversion Price. The Conversion Price for the Series A
         Preferred shall initially be equal to ninety-two percent (92%) of the
         Closing Price (as defined below) (the "CONVERSION PRICE"). Such initial
         Conversion Price shall be adjusted from time to time in accordance with
         this Section 4. All references to the Conversion Price herein shall
         mean the Conversion Price as so adjusted. The "CLOSING PRICE" shall be
         the lesser of (i) the average of the closing sale prices (or the
         closing bids, if no sales were reported) of the Common Stock as
         reported on The Nasdaq National Market for the five (5) trading days
         immediately preceding and ending on the last trading day prior to the
         date of execution of the Purchase Agreement and (ii) the average of the
         closing sale prices (or the closing bids, if no sales were reported) of
         the Common Stock as reported on The Nasdaq National Market for the five
         (5) trading days immediately preceding and ending on the last trading
         day prior to the date of the Company's stockholders meeting at which
         the issuance of the Series A Preferred is approved; provided, however,
         that if the Corporation has not effected a reverse stock split of the
         Corporation's outstanding Common Stock within the range of 1-for-8 to
         1-for 12 (the "Reverse Split") at least three (3) trading days prior to
         the beginning of the five (5) trading day range described in clause
         (ii) immediately above, then such five (5) trading day range shall not
         commence until the date that is the fourth trading day after the
         effectiveness of the Reverse Split."

         5. The first paragraph that is not printed completely in bold type of
the form of warrant attached as Exhibit B to the Agreement is hereby amended to
read in its entirety as follows:

                  "This certifies that_______________, or its permitted assigns
         (the "Holder"), for value received, is entitled to purchase from
         INTRABIOTICS PHARMACEUTICALS, INC., a Delaware corporation (the
         "Company"), having a place of business at 2483 East Bayshore Road,
         Suite 100, Palo Alto, California 94303, such aggregate maximum number
         of fully paid and nonassessable shares of the Company's Common Stock
         ("Common Stock") as would be obtained in accordance with the formula
         set forth below at a price equal to the Stock Purchase Price (as
         defined below) at any time or from time to time, subject to Section 1.1
         hereof, up to and including 5:00 p.m. (Pacific time) on __________,
         2008 (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 upon
         payment in cash or wire transfer 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 aggregate
         number of shares subject to this Warrant shall be equal to (i) 50% of
         the Holder's aggregate purchase price for the shares of Series A
         Convertible Preferred Stock (the "Series A Preferred") as set forth on
         the Signature Page (as defined therein) of that certain Preferred Stock
         and Warrant Purchase Agreement (the "Purchase
<PAGE>
         Agreement"), dated as of February 5, 2003 (the "Definitive Agreement
         Date"), between the Holder and the Company divided by (ii) ninety-two
         percent (92%) of the Stock Purchase Price. The "Stock Purchase Price"
         shall initially be equal to the lesser of (i) the average of the
         closing sale prices of the Common Stock on The Nasdaq National Market
         for the five (5) trading days immediately preceding and ending on the
         last trading day prior to the Definitive Agreement Date and (ii) the
         average of the closing sale prices of the Common Stock on The Nasdaq
         National Market for the five (5) trading days immediately preceding and
         ending on the last trading day prior to the Company's stockholders
         meeting at which the issuance of the Series A Preferred is approved;
         provided, however, that if the Company has not effected a reverse stock
         split of the Company's outstanding Common Stock within the range of
         1-for-8 to 1-for 12 (the "Reverse Split") at least three (3) trading
         days prior to the beginning of the five (5) trading day range described
         in clause (ii) immediately above, then such five (5) trading day range
         shall not commence until the date that is the fourth trading day after
         the effectiveness of the Reverse Split; provided further, that
         notwithstanding anything set forth herein to the contrary, in the event
         that the total number of shares of Series A Preferred (on an
         as-is-converted basis) issued or issuable pursuant to the Purchase
         Agreement is subject to the limitation of no greater than 19.9% of the
         Company's issued and outstanding shares of Common Stock on the date of
         the Purchase Agreement (in accordance with the requirements of The
         Nasdaq Stock Market for purposes of Rule 4350(i)(1)(D) thereof), then
         the Stock Purchase Price shall be equal to the closing bid price of the
         Common Stock on The Nasdaq Stock Market on the Definitive Agreement
         Date. The Stock Purchase Price and the number of shares purchasable
         hereunder are subject to adjustment as provided in Section 3 of this
         Warrant. As used herein, the term "Original Issue Date" shall mean the
         issuance date of this Warrant."

         6. The Agreement, as supplemented and modified by this Amendment,
together with the other writings referred to in the Agreement or delivered
pursuant thereto which form a part thereof, contain the entire agreement among
the parties with respect to the subject matter thereof and amend, restate and
supersede all prior and contemporaneous arrangements and understandings with
respect thereto.

         7. Upon the effectiveness of this Amendment, on and after the date
hereof, each reference in the Agreement to "this Agreement," "hereunder,"
"hereof," "herein" or words of like import, and each reference in the other
documents entered into in connection with the Agreement, shall mean and be a
reference to the Agreement as amended hereby. Except as specifically amended
above, the Agreement shall remain in full force and effect and is hereby
ratified and confirmed.

         8. This Amendment may be executed in any number of counterparts, each
of which shall be deemed to be an original instrument, but all of which when
taken together shall constitute but one agreement.
<PAGE>
         IN WITNESS WHEREOF, the parties hereto have executed this Amendment to
the Preferred Stock and Warrant Purchase Agreement as of the date set forth in
the first paragraph hereof.

<TABLE>
<S>                                                 <C>
COMPANY:                                            INVESTOR:

INTRABIOTICS PHARMACEUTICALS, INC.
                                                    --------------------------------------------
                                                             (Entity Name, if applicable)


Signature:                                          Signature:
          ---------------------------------                   ----------------------------------

Print Name:                                         Print Name:
           --------------------------------                    ---------------------------------

Title:                                              Title:
      -------------------------------------               --------------------------------------
</TABLE>