<PAGE>

                                                                     EXHIBIT 4.1

                          CERTIFICATE OF INCORPORATION
                                       OF
                           ELITE PHARMACEUTICALS, INC.


     The undersigned, for the purposes of forming a corporation under the laws
of the State of Delaware, do make, file and record this Certificate, and do
certify that:

     FIRST:     The name of this corporation is ELITE PHARMACEUTICALS, INC.

     SECOND:    Its Registered Office in the State of Delaware is to be located
at 9 East Loockerman Street, in the City of Dover, County of Kent, 19901. The
Registered Agent in charge thereof is National Registered Agents, Inc.

     THIRD:     The purpose of the corporation is to engage in lawful act or
activity for which a corporation may be organized under the General Corporation
Law of Delaware.

     FOURTH:    The amount of the total authorized capital stock of the
corporation is 20 million, all of which are of a par value of $.01 dollars each
and classified as Common stock.

     FIFTH:     The name and mailing address of the incorporator are as follows:

           NAME                            MAILING ADDRESS
           ----                            ---------------

           Theresa Lennon                  Intercounty Clearance Corporation
                                           111 Washington Avenue
                                           Albany, New York 12210

     SIXTH:     The duration of the corporation shall be perpetual.

     SEVENTH:   When a compromise or arrangement is proposed between the
corporation and its creditors or any class of them or between the corporation
and its shareholders or any class of them, a court of equity jurisdiction within
the state, on application of the corporation or of a creditor or shareholder
thereof, or on application of a receiver appointed for the corporation pursuant
to the provisions of Section 291 of Title 8 of the Delaware Code or on
application of trustees in dissolution or of any receiver or receivers appointed
for the corporation pursuant to provisions of Section 279 of Title 8 of the
Delaware Code order a meeting of the creditors or class of creditors or of the
shareholders or class of shareholders to be affected by the proposed compromise
or arrangement or reorganization, to be summoned in such manner as the court
directs. If a majority in number representing 3/4 in value of the creditors or
class of creditors, or of the shareholders or class of shareholders to be
affected by the proposed compromise or arrangement or a reorganization, agree to
a compromise or arrangement or a reorganization of the corporation as a
consequence of the compromise or arrangement, the compromise or arrangement and
the reorganization, if sanctioned by the court to which the application has been

<PAGE>

made, shall be binding on all the creditors or class of creditors, or on all the
shareholders or class of shareholders and also on the corporation.

     EIGHTH:    The personal liability of all of the directors of the
corporation is hereby eliminated to the fullest extent allowed as provided by
the Delaware General Corporation Law, as the same may be supplemented and
amended.

     NINTH:     The corporation shall, to the fullest extent legally permissible
under the provisions of the Delaware General Corporation Law, as the same may be
amended and supplemented, shall indemnify and hold harmless any and all persons
whom it shall have power to indemnify under said provisions from and against any
and all liabilities (including expenses) imposed upon or reasonably incurred by
him in connection with any action, suit or other proceeding in which he may be
involved or with which he may be threatened, or other matters referred to in or
covered by said provisions both as to action in his official capacity and as to
action in another capacity while holding such office, and shall continue as to a
person who has ceased to be a director or officer of the corporation. Such
indemnification provided shall not be deemed exclusive of any other rights to
which those indemnified may be entitled under any Bylaw, Agreement or Resolution
adopted by the shareholders entitled to vote thereon after notice.



Dated on this 1st day of October, 1997.



                                           /s/ Theresa Lennon
                                          -----------------------------
                                          Theresa Lennon, Incorporator


                            CERTIFICATE OF AMENDMENT
                                       OF
                          CERTIFICATE OF INCORPORATION
                                       OF
                           ELITE PHARMACEUTICALS, INC.


     ELITE PHARMACEUTICALS, INC., a corporation organized and existing under by
virtue of the General Corporation Law of the State of Delaware, DOES HEREBY
CERTIFY:

     The following Amendment to the Certificate of Incorporation, as set out
above, was approved and adopted by the consent of a majority of all the
shareholders entitled to vote thereon, and with written notice provided to those
shareholders that did not consent in writing, all as in accordance with Delaware
Statutes Annotated, Title 8, Section 242:

     RESOLVED, that the Certificate of Incorporation of Elite Pharmaceuticals,
     Inc. be amended by deleting ARTICLE FOURTH in its entirety and substituting
     the following:
<PAGE>

          FOURTH: The total number of shares of capital stock which the
          Corporation is authorized to issue is Ten Million (10,000,000), all of
          which have a par value of $.01, and all classified as Common Stock.
          Each share of Common Stock shall entitle the holder to vote on all
          matters upon which shareholders vote.

          Each two of the previously authorized, issued and outstanding
          14,750,200 shares of Common Stock, of the par value $.01 are hereby
          converted into and become one share of Common Stock, the par value of
          $.01 per share, and each option or warrant outstanding exercisable for
          two hares of the Common Stock shall be hereafter exercisable for one
          such share, each exercisable two times the exercise price for which
          the single share was previously exercisable.

     IN WITNESS WHEREOF, said Elite Pharmaceuticals, Inc. has caused this
certificate to be signed by Atul M. Mehta, its President and attested by
______________________, its _____________ Secretary, this 30th day of March,
1998.


[CORPORATE SEAL]                              ELITE PHARMACEUTICALS, INC.

Attest:                                       By:
                                                    --------------------------
                                                    Atul M. Mehta, President
----------------------
       Secretary
------
                            CERTIFICATE OF AMENDMENT
                                       OF
                          CERTIFICATE OF INCORPORATION
                                       OF
                           ELITE PHARMACEUTICALS, INC.

     ELITE PHARMACEUTICALS, INC., a corporation organized and existing under by
virtue of the General Corporation Law of the State of Delaware, DOES HEREBY
CERTIFY:

     The following Amendment to the Certificate of Incorporation, as set out
above, was approved and adopted by the consent of a majority of all the
shareholders entitled to vote thereon, and with written notice provided to those
shareholders that did not consent in writing, all as in accordance with Delaware
Statutes Annoted, Title 8, Section 242:

     RESOLVED, that the Certificate of Incorporation of Elite Pharmaceuticals,
     Inc. be amended by deleting ARTICLE FOURTH in its entirety and substituting
     the following:

          FOURTH: The total number of shares of capital stock which the
          Corporation is authorized to issue is Twenty-Five Million
          (25,000,000), all
<PAGE>

          of which have a par value of $.01, and all classified as Common Stock.
          Each share of Common Stock shall entitle the holder to vote on all
          matters upon which shareholders vote.

     IN WITNESS WHEREOF, said Elite Pharmaceuticals, Inc. has caused this
certificate to be signed by Atul M. Mehta, its President and attested by Ellen
Cianflone, its Assistant Secretary, this 28th day of May, 1998.



[CORPORATE SEAL]                                 ELITE PHARMACEUTICALS, INC.

Attest:                                          By:  /s/ Atul M. Mehta
                                                     --------------------------
 /s/ Ellen C. Cianflone                              Atul M. Mehta, President
---------------------------
Assistant Secretary