<PAGE>

================================================================================

                       SECURITIES AND EXCHANGE COMMISSION
                             Washington, DC 20549
                               ________________

                                  FORM 10-Q/A

                                AMENDMENT NO. 1

(Mark One)
 [x]             QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d)
                    OF THE SECURITIES EXCHANGE ACT OF 1934.

                 For the Quarterly Period Ended June 30, 2000.

                                      or

 [_]            TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d)
                    OF THE SECURITIES EXCHANGE ACT OF 1934.

           For the Transition Period from ___________ to __________.

                          Commission File No. 0-19651
                               ________________

                         MAGAININ PHARMACEUTICALS INC.
                         -----------------------------
            (Exact name of registrant as specified in its charter)


                Delaware                                   13-3445668
                --------                                   ----------
     (State or other jurisdiction of                      (IRS Employer
     incorporation or organization)                  Identification Number)

            5110 Campus Drive
       Plymouth Meeting, Pennsylvania                        19462
       ------------------------------                        -----
   (Address of principal executive offices)                (ZIP Code)


                                 610-941-4020
                                 ------------
             (Registrant's telephone number, including area code)


     Indicate by check mark whether the registrant (1) has filed all reports
required to be filed by Section 13 or 15(d) of the Securities Exchange Act of
1934 during the preceding 12 months (or for such shorter period that the
registrant was required to file such reports), and (2) has been subject to such
filing requirements for the past 90 days. Yes [x] No [_]

     The number of outstanding shares of the Registrant's Common Stock, par
value $.002 per share, on August 10, 2000 was 28,198,315.

================================================================================
<PAGE>

                         MAGAININ PHARMACEUTICALS INC.
                                AMENDMENT NO. 1
                                    TO THE
                         QUARTERLY REPORT ON FORM 10-Q
                      FOR THE QUARTER ENDED JUNE 30, 2000


PURPOSE OF AMENDMENT

  The purpose of Amendment No. 1 is to refile Exhibit 10.1. Portions of this
Exhibit have been omitted and filed separately with the Securities and Exchange
Commission pursuant to an application for confidential treatment filed with the
Securities and Exchange Commission pursuant to Rule 24b-2 under the Securities
Act of 1934, as amended. The Registrant hereby also amends Item 6 of its
Quarterly Report on Form 10-Q, as set forth in the pages attached hereto.

                                       2
<PAGE>

ITEM 6.   EXHIBITS AND REPORTS ON FORM 8-K

   (a)    Exhibits

          10.1   License and Collaboration Agreement between Magainin
                 Pharmaceuticals Inc. and Genentech, Inc. dated April 28,
                 2000.*+

          10.2   Certificate of Designations, Preferences and Rights of Series A
                 Preferred Stock of Magainin Pharmaceuticals Inc. dated May 8,
                 2000.(1)

          10.3   Stock Purchase Agreement between Magainin Pharmaceuticals Inc.
                 and Genentech, Inc. dated April 28, 2000.(1)

          10.4   Registration Rights Agreement between Magainin Pharmaceuticals
                 Inc. and Genentech, Inc. dated April 28, 2000.(1)

          27.1   Financial data schedule for the six-month period ended June 30,
                 2000 (electronic filing only).(1)

     (b)  Reports on Form 8-K

          We filed a Current Report on Form 8-K on May 9, 2000 regarding the
          execution of a collaborative agreement and financing arrangement
          agreements between us and Genentech, Inc.


_______________

*    Filed herewith.

+    Confidential treatment has been requested as to certain portions of this
     exhibit. The omitted portions have been separately filed with the
     Securities and Exchange Commission.
(1)  Previously filed with the Quarterly Report on Form 10-Q filed on
     August 14, 2000.

                                       3

<PAGE>

                                  SIGNATURES

     Pursuant to the requirements of the Securities Exchange Act of 1934, the
registrant has duly caused this report to be signed on its behalf by the
undersigned thereunto duly authorized.


                                        MAGAININ PHARMACEUTICALS INC.



Date:  October 11, 2000                 By: /s/ Michael R. Dougherty
                                           ---------------------------------
                                           Michael R. Dougherty
                                           President and Chief Executive Officer


Date:  October 11, 2000                 By: /s/ Christopher P. Schnittker
                                           ---------------------------------
                                           Christopher P. Schnittker
                                           Vice President and Chief Financial
                                           Officer

                                       4
<PAGE>

                                 EXHIBIT INDEX

Exhibit No.      Description
-----------      -----------

     10.1      License and Collaboration Agreement between Magainin
               Pharmaceuticals Inc. and Genentech, Inc. dated April 28, 2000.*+

     10.2      Certificate of Designations, Preferences and Rights of Series A
               Preferred Stock of Magainin Pharmaceuticals Inc. dated May 8,
               2000. (1)

     10.2      Stock Purchase Agreement between Magainin Pharmaceuticals Inc.
               and Genentech, Inc. dated April 28, 2000. (1)

     10.3      Registration Rights Agreement between Magainin Pharmaceuticals
               Inc. and Genentech, Inc. dated April 28, 2000. (1)

     27.1      Financial data schedule for the six-month period ended June 30,
               2000 (electronic filing only). (1)

______________

*    Filed herewith.

+    Confidential treatment has been requested as to certain portions of this
     exhibit. The omitted portions have been separately filed with the
     Securities and Exchange Commission.

(1)  Previously filed with the Quarterly Report on Form 10-Q filed on August 14,
     2000.