<PAGE>

                                                                    Exhibit 3.1

                     RESTATED CERTIFICATE OF INCORPORATION

                                       OF

                      APPLIED ANALYTICAL INDUSTRIES, INC.

                        PURSUANT TO SECTIONS 242 AND 245
                         OF THE GENERAL CORPORATION LAW
                            OF THE STATE OF DELAWARE

         APPLIED ANALYTICAL INDUSTRIES, INC., (the "Corporation"), a
corporation organized and existing under and by virtue of the General
Corporation Law of the State of Delaware (the "General Corporation Law"),
hereby certifies as follows:

         1.       The name of the Corporation is Applied Analytical Industries,
Inc. The original Certificate of Incorporation was filed with the Secretary of
State of Delaware on September 29, 1986.

         2.       Pursuant to Section 103(d) of the General Corporation Law,
this Restated Certificate of Incorporation shall become effective at 10:00
a.m., Wilmington, Delaware time, on September 25, 1996.

         3.       This Restated Certificate of Incorporation: (a) restates and
integrates and further amends the Restated Certificate of Incorporation of the
Corporation that was filed on June 7, 1996, (b) was duly adopted in accordance
with the provisions of Section 242 and 245 of the General Corporation Law and
(c) was approved by written consent of the stockholders of the Corporation
given in accordance with the provisions of Section 228 of the General
Corporation Law (prompt notice of such action having been given to those
stockholders who did not consent in writing). The text of the Corporation's
Certificate of Incorporation as previously amended, supplemented or restated is
hereby further restated and further amended to read in its entirety as follows:

         FIRST.  The name of the Corporation is:

                      Applied Analytical Industries, Inc.

         SECOND. The address of its registered office in the State of Delaware
is Corporation Trust Center, 1209 Orange Street, in the City of Wilmington,
County of New Castle. The name of its registered agent at such address is The
Corporation Trust Company.

         THIRD. The nature of the business or purposes to be conducted or
promoted by the Corporation is as follows:

<PAGE>

                  To engage in any lawful act or activity for which
         corporations may be organized under the General Corporation Law of
         Delaware.

         FOURTH. The total number of shares of all classes of stock that the
Corporation shall have authority to issue is 105,000,000 shares, consisting of
(i) 100,000,000 shares of Common Stock, $.001 par value per share ("Common
Stock"), and (ii) 5,000,000 shares of Preferred Stock, $.001 par value per
share ("Preferred Stock").

         The following is a statement of the designations and the powers,
privileges and rights, and the qualifications, limitations or restrictions
thereof in respect of each class of capital stock of the Corporation.

A.       COMMON STOCK

         1.       General. The voting, dividend and liquidation rights of the
holders of the Common Stock are subject to and qualified by the rights of the
holders of the Preferred Stock of any series as may be designated by the Board
of Directors upon any issuance of the Preferred Stock of any series.

         2.       Voting. The holders of the Common Stock are entitled to one
vote for each share held at all meetings of stockholders (and written actions
in lieu of meetings). There shall be no cumulative voting.

         The number of authorized shares of Common Stock may be increased or
decreased (but not below the number of shares thereof then outstanding) by the
affirmative vote of the holders of a majority of the stock of the Corporation
entitled to vote, irrespective of the provisions of Section 242(b)(2) of the
General Corporation Law.

         3.       Dividends. Dividends may be declared and paid on the Common
Stock from funds lawfully available therefor as and when determined by the
Board of Directors and subject to any preferential dividend rights of any then
outstanding Preferred Stock.

         4.       Liquidation. Upon the dissolution or liquidation of the
Corporation, whether voluntary or involuntary, holders of Common Stock will be
entitled to receive all assets of the Corporation available for distribution to
its stockholders, subject to any preferential rights of any then outstanding
Preferred Stock.

B.       PREFERRED STOCK.

         Preferred Stock may be issued from time to time in one or more series,
each of such series to have such terms as stated or expressed herein and in the
resolution or resolutions providing for the issue of such series adopted by the
Board of Directors of the Corporation as hereinafter provided. Any shares of
Preferred Stock that may be redeemed, purchased or acquired by the Corporation
may be reissued except as otherwise provided by law or this Certificate of
Incorporation. Different series of Preferred Stock shall not be construed to

<PAGE>

constitute different classes of shares for the purposes of voting by classes
unless expressly provided.

         Authority is hereby expressly granted to the Board of Directors from
time to time to issue the Preferred Stock in one or more series, and in
connection with the creation of any such series, by resolution or resolutions
providing for the issue of the shares thereof, to determine and fix such voting
powers, full or limited, or no voting powers, and such designations,
preferences and relative participating, optional or other special rights, and
qualifications, limitations or restrictions thereof, including without
limitation, dividend rights, conversion rights, redemption privileges and
liquidation preferences, as shall be stated and expressed in such resolutions,
all to the full extent now or hereafter permitted by the General Corporation
Law. Without limiting the generality of the foregoing, the resolutions
providing for issuance of any series of Preferred Stock may provide that such
series shall be superior or rank equally or be junior to the Preferred Stock of
any other series to the extent permitted by law and this Certificate of
Incorporation. Except as otherwise provided in this Certificate of
Incorporation, no vote of the holders of the Preferred Stock or Common Stock
shall be a prerequisite to the designation or issuance of any shares of any
series of the Preferred Stock authorized by and complying with the conditions
of this Certificate of Incorporation, the right to have such vote being
expressly waived by all present and future holders of the capital stock of the
Corporation.

         FIFTH. The Corporation shall have a perpetual existence.

         SIXTH. In furtherance of and not in limitation of powers conferred by
statute, the board of directors is expressly authorized to adopt, amend or
repeal the by-laws of the Corporation.

         SEVENTH. Whenever a compromise or arrangement is proposed between this
Corporation and its creditors or any class of them and/or between this
Corporation and its stockholders or any class of them, any court of equitable
jurisdiction within the State of Delaware may, on the application in a summary
way of this Corporation or of any creditor or stockholder thereof, or on the
application of any receiver or receivers appointed for this Corporation under
the provisions of Section 291 of Title 8 of the Delaware Code or on the
application of trustees in dissolution or of any receiver or receivers
appointed for this Corporation under the provisions of section 279 of Title 8
of the Delaware Code order a meeting of the creditors or class of creditors,
and/or of the stockholders or class of stockholders of this Corporation, as the
case may be, to be summoned in such manner as the said court directs. If a
majority in number representing three-fourths in value of the creditors or
class of creditors, and/or of the stockholders or class of stockholders of this
Corporation, as the case may be, agree to any compromise or arrangement and to
any reorganization of this Corporation as a consequence of such compromise or
arrangement, the said compromise or arrangement and the said reorganization
shall, if sanctioned by the court to which the said application has been made,
be binding on all the creditors or class of creditors, and/or on all the
stockholders or class of stockholders, of this Corporation, as the case may be,
and also on this Corporation.

         EIGHTH. Except to the extent that the General Corporation Law
prohibits the elimination or limitation of liability of directors for breaches
of fiduciary duty, no director of the Corporation shall be personally liable to
the Corporation or its stockholders for monetary

<PAGE>

damages for any breach of fiduciary duty as a director, notwithstanding any
other provision of law imposing such liability. No amendment to or repeal of
this provision shall apply to or have any effect on the liability or alleged
liability of any director of the Corporation for or with respect to any acts or
omissions of such director occurring prior to such amendment.

         NINTH. The Corporation reserves the right to amend, alter, change or
repeal any provision contained in this Restated Certificate of Incorporation,
in the manner now or hereafter prescribed by statute and this Restated
Certificate of Incorporation, and all rights conferred upon stockholders herein
are granted subject to this reservation.

         TENTH: This Article is inserted for the management of the business and
for the conduct of the affairs of the Corporation.

         1.       Number of Directors. The number of directors of the
Corporation shall not be less than three (3) nor more than seven (7). The exact
number of directors within the limitations specified in the preceding sentence
shall be fixed from time to time by, or in the manner provided in, the
Corporation's By-Laws.

         2.       Classes of Directors. The Board of Directors shall be and is
divided into three classes: Class I, Class II and Class III. No one class shall
have more than one director more than any other class. If a fraction is
contained in the quotient arrived at by dividing the designated number of
directors by three, then, if such fraction is one-third, the extra director
shall be a member of Class I, and if such fraction is two-thirds, one of the
extra directors shall be a member of Class I and one of the extra directors
shall be a member of Class II, unless otherwise provided from time to time by
resolution adopted by the Board of Directors.

         3.       Election of Directors. Elections of directors must be by
written ballot.

         4.       Terms of Office. Each director shall serve for a term ending
on the date of the third annual meeting following the annual meeting at which
such director was elected; provided, that each initial director in Class I
shall serve for a term ending on the date of the annual meeting in 1997; each
initial director in Class II shall serve for a term ending on the date of the
annual meeting in 1998; and each initial director in Class III shall serve for
a term ending on the date of the annual meeting in 1999; and provided further,
that the term of each director shall be subject to the election and
qualification of his successor and to his earlier death, resignation or
removal.

         5.       Allocation of Directors Among Classes in the Event of
Increases or Decreases in the Number of Directors. In the event of any increase
or decrease in the authorized number of directors, (i) each director then
serving as such shall nevertheless continue as a director of the class of which
he is a member and (ii) the newly created or eliminated directorships resulting
from such increase or decrease shall be apportioned by the Board of Directors
among the three classes of directors so as to ensure that no one class has more
than one director more than any other class. To the extent possible, consistent
with the foregoing rule, any newly created directorships shall be added to
those classes whose terms of office are to expire at the latest dates following
such allocation, and any newly eliminated directorships shall be subtracted
from those

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classes whose terms of offices are to expire at the earliest dates following
such allocation, unless otherwise provided from time to time by resolution
adopted by the Board of Directors.

         6.       Quorum; Action at Meeting. A majority of the directors at any
time in office shall constitute a quorum for the transaction of business. In
the event one or more of the directors shall be disqualified to vote at any
meeting, then the required quorum shall be reduced by one for each director so
disqualified, provided that in no case shall less than one-third of the number
of directors fixed pursuant to Section 1 above constitute a quorum. If at any
meeting of the Board of Directors there shall be less than such a quorum, a
majority of those present may adjourn the meeting from time to time. Every act
or decision done or made by a majority of the directors present at a meeting
duly held at which a quorum is present shall be regarded as the act of the
Board of Directors unless a greater number is required by law, by the By-Laws
of the Corporation or by this Restated Certificate of Incorporation.

         7.       Resignation; Removal. Any director may resign at any time
upon written notice to the attention of the secretary of the corporation.
Directors of the Corporation may be removed only for cause by the affirmative
vote of the holders of at least two-thirds of the shares of the capital stock
of the Corporation issued and outstanding and entitled to vote.

         8.       Vacancies. Any vacancy in the Board of Directors, however
occurring, including a vacancy resulting from an enlargement of the board,
shall be filled only by a vote of a majority of the directors then in office,
although less than a quorum, or by a sole remaining director. A director
elected to fill a vacancy shall be elected to hold office until the next
election of the class for which such director shall have been chosen, subject
to the election and qualification of his successor and to his earlier death,
resignation or removal.

         9.       Amendments to Article. Notwithstanding any other provisions
of law, this Restated Certificate of Incorporation or the By-Laws of the
Corporation, each as amended, and notwithstanding the fact that a lesser
percentage may be specified by law, the affirmative vote of the holders of at
least seventy-five percent (75%) of the shares of capital stock of the
Corporation issued and outstanding and entitled to vote shall be required to
amend or repeal, or to adopt any provision inconsistent with, this Article
TENTH.

         ELEVENTH. Stockholders of the Corporation may not take any action by
written consent in lieu of a meeting. Notwithstanding any other provisions of
law, this Restated Certificate of Incorporation or the By-Laws of the
Corporation, each as amended, and notwithstanding the fact that a lesser
percentage may be specified by law, the affirmative vote of the holders of at
least seventy-five percent (75%) of the shares of capital stock of the
Corporation issued and outstanding and entitled to vote shall be required to
amend or repeal, or to adopt any provision inconsistent with, this Article
ELEVENTH.

         TWELFTH. Special meetings of stockholders may be called at any time by
(and only by) the Board of Directors. Business transacted at any special
meeting of stockholders shall be limited to matters relating to the purpose or
purposes stated in the notice of meeting. Notwithstanding any other provision
of law, this Restated Certificate of Incorporation or the By-Laws of the
Corporation, each as amended, and notwithstanding the fact that a lesser
percentage

<PAGE>

may be specified by law, the affirmative vote of the holders of at least
seventy-five percent (75%) of the shares of capital stock of the Corporation
issued and outstanding and entitled to vote shall be required to amend or
repeal, or to adopt any provisions inconsistent with, this Article TWELFTH.

         THIRTEENTH. In anticipation that the Corporation may enter into
contracts or otherwise transact business with entities in which any directors
of the Corporation own a financial interest ("Related Entities"), the
provisions of this Article THIRTEENTH are set forth to regulate and guide such
contracts or other business. These provisions are in addition to, and not in
limitation of, the provisions of the General Corporation Law and the other
provisions of this Restated Certificate of Incorporation. Any contract or other
business that does not comply with the procedures set forth in this Article
THIRTEENTH shall not by reason thereof be deemed void or voidable or result in
any breach of any duty or the derivation of any improper personal benefit by
any person but shall be governed by the provisions of this Restated Certificate
of Incorporation, the By-laws of the Corporation, the General Corporation Law
and other applicable law.

         No contract, agreement, arrangement or transaction between the
Corporation and a Related Entity (a "Related Transaction") shall be void or
voidable solely for the reason that such persons or entities are parties
thereto, if:

         (i)      the material facts of the Related Transaction are disclosed
                  or are known to the Board of Directors of the Corporation (or
                  a committee thereof) and such board (or committee) in good
                  faith authorizes, approves or ratifies the Related
                  Transaction by the affirmative vote of a majority of the
                  disinterested directors on the Board of Directors (or such
                  committee), even though the disinterested directors may be
                  less than a quorum;

         (ii)     the material facts of the Related Transaction are disclosed
                  or are known to the holders of the then outstanding voting
                  shares of the Corporation entitled to vote thereon, and the
                  Related Transaction is specifically approved or ratified in
                  good faith by the affirmative vote of the holders of a
                  majority of the then outstanding voting shares not owned by
                  the interested directors or Related Entity, as the case may
                  be, even though such holders may be less than a quorum;

         (iii)    such Related Transaction is effected pursuant to and
                  consistent with terms and conditions specified in any
                  arrangements, standards or guidelines that are in good faith
                  authorized, approved or ratified, after disclosure or
                  knowledge of the material facts related thereto, by the
                  affirmative vote of a majority of the disinterested directors
                  on the Board of Directors (or committee thereof), or by the
                  affirmative vote of the holders of a majority of the then
                  outstanding voting shares of the Corporation not owned by the
                  interested directors or Related Entity, as the case may be,
                  even though the disinterested directors or such holders may
                  be less than a quorum; or

         (iv)     The Related Transaction was fair to the Company.

<PAGE>

         In addition, each Related Transaction authorized, approved or
effected, and each of such arrangements, standards or guidelines so authorized
or approved, as described in (i), (ii) or (iii) above, shall be conclusively
deemed to be fair to the Corporation and its stockholders; provided, however,
that if such authorization or approval is not obtained, or such Related
Transaction is not so effected, no presumption shall arise that such Related
Transaction, or such arrangements, standards or guidelines, are not fair to the
Corporation and its stockholders.

         Any person or entity purchasing or otherwise acquiring any interest in
any shares of the Corporation shall be deemed to have notice of and to have
consented to the provisions of this Article THIRTEENTH.

         IN WITNESS WHEREOF, Applied Analytical Industries, Inc. has caused
this Restated Certificate of Incorporation to be signed and attested by its
duly authorized officers, this 20th day of September, 1996.

                                      APPLIED ANALYTICAL INDUSTRIES, INC.



                                      By:        /s/ Frederick D. Sancilio
                                               --------------------------------
                                               Frederick D. Sancilio, President

ATTEST:



  /s/ R. Forrest Waldon
----------------------------
R. Forrest Waldon, Secretary

<PAGE>

                           CERTIFICATE OF AMENDMENT
                                       OF
                          CERTIFICATE OF INCORPORATION
                                       OF
                      APPLIED ANALYTICAL INDUSTRIES, INC.

         Applied Analytical Industries, Inc., a corporation organized and
existing under and by virtue of the General Corporation Law of the State of
Delaware, DOES HEREBY CERTIFY:

         FIRST: That the Board of Directors of said corporation, duly adopted a
resolution setting forth a proposed amendment of the Certificate of
Incorporation of said corporation, declaring said amendment to be advisable,
and calling a meeting of the stockholders of said corporation for consideration
thereof. The resolution setting forth the proposed amendment is as follows:

                  RESOLVED, that the Certificate of Incorporation of Applied
                  Analytical Industries, Inc. be amended to increase the
                  maximum size of the Board of Directors from seven (7) to nine
                  (9).

         SECOND: That thereafter, a meeting of the stockholders of said
corporation was duly called and held, upon notice in accordance with Section
222 of the General Corporation Law of the State of Delaware at which meeting
the holders of more than 75% of the outstanding shares of voting stock voted in
favor of the amendment.

         THIRD: That the aforesaid amendments were duly adopted in accordance
with the applicable provisions of Sections 242 and 222 of the General
Corporation Law of the State of Delaware.

<PAGE>

         IN WITNESS WHEREOF, said Applied Analytical Industries, Inc. has
caused this certificate to be signed by Frederick D. Sancilio, Ph.D., its
Chairman of the Board of Directors, this 24th day of May, 2000.


                                            APPLIED ANALYTICAL INDUSTRIES, INC.



                                            By:/s/ Frederick D. Sancilio
                                               ---------------------------------
                                               Frederick D. Sancilio, President

<PAGE>

                            CERTIFICATE OF AMENDMENT
                                       OF
                          CERTIFICATE OF INCORPORATION
                                       OF
                      APPLIED ANALYTICAL INDUSTRIES, INC.

         Applied Analytical Industries, Inc., a corporation organized and
existing under and by virtue of the General Corporation Law of the State of
Delaware, DOES HEREBY CERTIFY:

         FIRST: That the Board of Directors of said corporation, duly adopted a
resolution setting forth a proposed amendment of the Certificate of
Incorporation of said corporation, declaring said amendment to be advisable,
and calling a meeting of the stockholders of said corporation for consideration
thereof. The resolution setting forth the proposed amendment is as follows:

                  RESOLVED, that Article First of the Corporation's Certificate
                  of Incorporation is hereby deleted in its entirety and
                  replaced with the following new Article First:

                           "First: The name of the Corporation is aaiPharma
                           Inc."

         SECOND: That thereafter, a meeting of the stockholders of said
corporation was duly called and held, upon notice in accordance with Section
222 of the General Corporation Law of the State of Delaware at which meeting
the holders of a majority of the outstanding shares of voting stock voted in
favor of the amendment.

         THIRD: That the aforesaid amendment was duly adopted in accordance
with the applicable provisions of Sections 242 and 222 of the General
Corporation Law of the State of Delaware.

<PAGE>

         IN WITNESS WHEREOF, said Applied Analytical Industries, Inc. has
caused this certificate to be signed by Frederick D. Sancilio, Ph.D., its
Chairman of the Board of Directors, this 15th day of November, 2000.


                                   APPLIED ANALYTICAL INDUSTRIES, INC.



                                   By:        /s/ Frederick D. Sancilio
                                            ----------------------------------
                                            Frederick D. Sancilio, Ph.D.
                                            Chairman of the Board of Directors

<PAGE>

                            CERTIFICATE OF AMENDMENT
                                       OF
                          CERTIFICATE OF INCORPORATION
                                       OF
                                 AAIPHARMA INC.

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

         FIRST: That the Board of Directors of said corporation, duly adopted a
resolution setting forth a proposed amendment of the Certificate of
Incorporation of said corporation, declaring said amendment to be advisable,
and calling a meeting of the stockholders of said corporation for consideration
thereof. The resolution setting forth the proposed amendment is as follows:

                  RESOLVED, that the Certificate of Incorporation of aaiPharma
                  Inc. be amended to increase the maximum size of the Board of
                  Directors from nine (9) to ten (10).

         SECOND: That thereafter, a meeting of the stockholders of said
corporation was duly called and held, upon notice in accordance with Section
222 of the General Corporation Law of the State of Delaware at which meeting
the holders of more than 75% of the outstanding shares of voting stock voted in
favor of the amendment.

         THIRD: That the aforesaid amendments were duly adopted in accordance
with the applicable provisions of Sections 242 and 222 of the General
Corporation Law of the State of Delaware.

         FOURTH: That Section 1 of the Tenth Article of the corporation's
Certificate of Incorporation is hereby amended and replaced in its entirety as
follows:

                  "1.      Number of Directors. The number of directors of the
Corporation shall not be less than three (3) nor more than ten (10)."

<PAGE>

         IN WITNESS WHEREOF, said aaiPharma Inc. has caused this certificate to
be signed by Frederick D. Sancilio, Ph.D., its Chairman of the Board of
Directors, this 27th day of June, 2002.


                                  AAIPHARMA INC.



                                  By:        /s/ Frederick D. Sancilio
                                           ----------------------------------
                                           Frederick D. Sancilio, Ph.D.
                                           Chairman of the Board of Directors
<PAGE>



                            CERTIFICATE OF AMENDMENT
                                       OF
                          CERTIFICATE OF INCORPORATION
                                       OF
                                 AAIPHARMA INC.

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

         FIRST: That the Board of Directors of said corporation, duly adopted a
resolution setting forth a proposed amendment of the Certificate of
Incorporation of said corporation, declaring said amendment to be advisable, and
calling a meeting of the stockholders of said corporation for consideration
thereof. The resolution setting forth the proposed amendment is as follows:

         RESOLVED, that the Certificate of Incorporation of aaiPharma
         Inc. be amended to increase the maximum size of the Board of
         Directors from ten (10) to twelve (12).

         SECOND: That thereafter, a meeting of the stockholders of said
corporation was duly called and held, upon notice in accordance with Section 222
of the General Corporation Law of the State of Delaware at which meeting the
holders of more than 75% of the outstanding shares of voting stock voted in
favor of the amendment.

         THIRD: That the aforesaid amendments were duly adopted in accordance
with the applicable provisions of Sections 242 and 222 of the General
Corporation Law of the State of Delaware.


<PAGE>




         IN WITNESS WHEREOF, said aaiPharma Inc. has caused this certificate to
be signed by Philip S. Tabbiner, its Chief Executive Officer and President, this
30th day of July, 2003.
                                          AAIPHARMA INC.


                                      By: /S/ Philip S. Tabbiner
                                          Philip S. Tabbiner, D.B.A.
                                          Chief Executive Officer and President