<PAGE>   1

                                                                     EXHIBIT 3.1

                                    RESTATED
                          CERTIFICATE OF INCORPORATION
                                       OF
                         INTERNET SECURITY SYSTEMS, INC.

                         (PURSUANT TO SECTION 245 OF THE
                GENERAL CORPORATION LAW OF THE STATE OF DELAWARE)



                  Internet Security Systems, Inc. (the "Corporation"), a
corporation organized and existing under and by virtue of the provisions of the
General Corporation Law of the State of Delaware (the "General Corporation
Law"),

                  DOES HEREBY CERTIFY:

         FIRST:            That the Corporation was originally incorporated
pursuant to the General Corporation Law on December 8, 1997 under the name "ISS
Group, Inc.";

         SECOND:           That the Restated Certificate of Incorporation (the
"Restated Certificate") in the form set forth below has been duly adopted in
accordance with the provisions of Section 245 of the General Corporation Law by
the directors of the Corporation;

         THIRD:            That the Restated Certificate only restates and
integrates and does not further amend the provisions of the Corporation's
Certificate of Incorporation, as amended to date, and there is no discrepancy
between the provisions of this Restated Certificate and those of the
Corporation's Certificate of Incorporation;

         FOURTH:           That, as permitted under Section 245 of the General
Corporation Law, the Restated Certificate removes the reference to the
incorporator of the Corporation and removes all references to the Series A
Preferred and Series B Preferred Stock, as such shares no longer exist, but does
not otherwise change the provisions applicable to the Corporation's authorized
but unissued shares of preferred stock; and

         FIFTH:            That the Restated Certificate so adopted reads in its
entirety as follows:

                                   ARTICLE I.

                  The name of this Corporation is: Internet Security Systems,
Inc.

                                   ARTICLE II.

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


<PAGE>   2

                                  ARTICLE III.

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


                                   ARTICLE IV.


         A.       Authorized Shares. The aggregate number of shares that the
         Corporation shall have authority to issue is 140,000,000, (i)
         120,000,000 shares of which shall be Common Stock, with a par value of
         $0.001 per share, and (ii) 20,000,000 shares of which shall be
         Preferred Stock, with a par value of $0.001 per share.

         B.       Common Stock. Each share of Common Stock shall have one vote
         on each matter submitted to a vote of the stockholders of the
         Corporation. Subject to the provisions of applicable law and the rights
         of the holders of outstanding shares of Preferred Stock, if any, the
         holders of shares of Common Stock shall be entitled to receive, when
         and as declared by the Board of Directors of the Corporation, out of
         the assets of the Corporation legally available therefor, dividends or
         other distributions, whether payable in cash, property or securities of
         the Corporation. The holders of shares of Common Stock shall be
         entitled to receive, in proportion to the number of shares of Common
         Stock held, the net assets of the Corporation upon dissolution after
         any preferential amounts required to be paid or distributed to holders
         of outstanding shares of Preferred Stock, if any, are so paid or
         distributed.

         C.       Preferred Stock. The Preferred Stock may be issued from time
         to time by the Board of Directors as shares of one or more series. The
         description of shares of each series of Preferred Stock, including any
         designations, preferences, conversion and other rights, voting powers,
         restrictions, limitations as to dividends, qualifications, and terms
         and conditions of redemption shall be as set forth in resolutions
         adopted by the Board of Directors.

                  Subject to the designation of rights, preferences,
         qualifications, limitations and restrictions of any issued and
         outstanding share of Preferred Stock, the Board of Directors is
         expressly authorized, at any time, by adopting resolutions providing
         for the issuance of, or providing for a change in the number of, shares
         of any particular series of Preferred Stock, and, if and to the extent
         from time to time required by law, by filing certificates of amendment
         or designation which are effective without stockholder action, to
         increase or decrease the number of shares included in each series of
         Preferred Stock, but not below the number of shares then issued, and to
         set in any one or more respects the designations, preferences,
         conversion or other rights, voting powers, restrictions, limitations as
         to dividends, qualifications, or terms and conditions of redemption
         relating to the shares of each such series. The authority of the Board
         of Directors with respect to each series of Preferred Stock shall
         include, but not be limited to, setting or changing the following:


                                       2
<PAGE>   3

                  a. the dividend rate, if any, on shares of such series, the
         times of payment and the date from which dividends shall be
         accumulated, if dividends are to be cumulative;

                  b. whether the shares of such series shall be redeemable and,
         if so, the redemption price and the terms and conditions of such
         redemption;

                  c. the obligation, if any, of the Corporation to redeem shares
         of such series pursuant to a sinking fund;

                  d. whether shares of such series shall be convertible into, or
         exchangeable for, shares of stock of any other class or classes and, if
         so, the terms and conditions of such conversion or exchange, including
         the price or prices or the rate or rates of conversion or exchange and
         the terms of adjustment, if any;

                  e. whether the shares of such series shall have voting rights,
         in addition to the voting rights provided by law, and, if so, the
         extent of such voting rights;

                  f. the rights of the shares of such series in the event of
         voluntary or involuntary liquidation, dissolution or winding up of the
         Corporation; and

                  g. any other relative rights, powers, preferences,
         qualifications, limitations or restrictions thereof relating to such
         series.

         D.       Shares Acquired by the Corporation. Shares of Common Stock
         that have been acquired by the Corporation shall become treasury shares
         and may be resold or otherwise disposed of by the Corporation for such
         consideration, not less than the par value thereof, as shall be
         determined by the Board of Directors, unless or until the Board of
         Directors shall by resolution provide that any or all treasury shares
         so acquired shall constitute authorized, but unissued shares.

                                   ARTICLE V.

         A director of the Corporation shall not be personally liable to the
Corporation or its stockholders for monetary damages for breach of fiduciary
duty as a director, except for liability (i) for any breach of the director's
duty of loyalty to the Corporation or its stockholders, (ii) for acts or
omissions not in good faith or which involve intentional misconduct or a knowing
violation of law, (iii) under Section 174 of the Delaware General Corporation
Law, or (iv) for any transaction from which the director derived any improper
personal benefit. If the Delaware General Corporation Law is amended after
approval by the stockholders of this Article to authorize Corporation action
further eliminating or limiting the personal liability of directors, then the
liability of a director of the Corporation shall be eliminated or limited to the
fullest extent permitted by the Delaware General Corporation Law as so amended.


                                       3
<PAGE>   4

                                   ARTICLE VI.

                  The management of the business and the conduct of the affairs
of the Corporation shall be vested in its Board of Directors. The number of
directors which shall constitute the whole Board of Directors shall be fixed by,
or in the manner provided in, the Bylaws of the Corporation.

                                  ARTICLE VII.

                  Meetings of stockholders may be held within or without the
State of Delaware, as the Bylaws may provide. The books of the Corporation may
be kept (subject to any provision contained in the statutes) outside the State
of Delaware at such place or places as may be designated from time to time by
the Board of Directors or in the Bylaws of the Corporation.


                                  ARTICLE VIII.

                  Election of directors at an annual or special meeting of
stockholders need not be by written ballot unless the Bylaws of the Corporation
shall so provide.


                                   ARTICLE IX.

         A.       At each annual meeting of stockholders, directors of the
Corporation shall be elected to hold office until the expiration of the term for
which they are elected, and until their successors have been duly elected and
qualified; except that if any such election shall not be so held, such election
shall take place at a stockholders' meeting called and held in accordance with
the Delaware General Corporation Law. The directors of the Corporation shall be
divided into three classes as nearly equal in size as is practicable, hereby
designated as Class I, Class II and Class III. The term of office of the initial
Class I directors shall expire at the 1999 annual meeting of stockholders, the
term of office of the initial Class II directors shall expire at the 2000 annual
meeting of stockholders and the term of office of the initial Class III
directors shall expire at the 2001 annual meeting of stockholders. At each
annual meeting, directors to replace those of a Class whose terms expire at such
annual meeting shall be elected to hold office until the third succeeding annual
meeting and until their respective successors shall have been duly elected and
qualified. If the number of directors is hereafter changed, any newly created
directorships or decrease in directorships shall be so apportioned among the
classes as to make all classes as nearly equal in number as is practicable.

         B.       Vacancies occurring on the Board of Directors for any reason
may be filled by vote of a majority of the remaining members of the Board of
Directors, although less than a quorum, at a meeting of the Board of Directors.
A person so elected by the Board of Directors to fill a vacancy shall hold
office until the next succeeding annual meeting of stockholders of the
Corporation and until his or her successor shall have been duly elected and
qualified.


                                       4
<PAGE>   5

                                   ARTICLE X.

                  In furtherance and not in limitation of the powers conferred
by statute, the Board of Directors is expressly authorized to make, alter, amend
or repeal the Bylaws of the Corporation.


                                   ARTICLE XI.

                  Stockholders of the Corporation may not take action by written
consent in lieu of a meeting, but must take any actions at a duly called annual
or special meeting.

                                  ARTICLE XII.

                  Notwithstanding any other provisions of this Certificate of
Incorporation or any provision of law which might otherwise permit a lesser vote
or no vote, but in addition to any affirmative vote of the holders of the
capital stock required by law or this Certificate of Incorporation, the
affirmative vote of the holders of at least two-thirds (2/3) of the combined
voting power of all of the then-outstanding shares of the Corporation entitled
to vote shall be required to alter, amend or repeal Articles IX, XI or XII or
any provisions thereof, unless such amendment shall be approved by a majority of
the directors of the Corporation not affiliated or associated with any person or
entity holding (or which has announced an intention to obtain) 26% or more of
the voting power of the Corporation's outstanding capital stock.

                                  ARTICLE XIII.

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


                                      * * *

                  IN WITNESS WHEREOF, Internet Security Systems, Inc. has caused
this Restated Certificate of Incorporation to be signed by its duly authorized
and elected Assistant Secretary this 20th day of October 2000.


                                                 INTERNET SECURITY SYSTEMS, INC.


                                                 By:          /s/ Sean Bowen
                                            ------------------------------------

                                                 Name:     Sean Bowen
                                                 Title:    Assistant Secretary


                                       5