<PAGE>
                                                                       EXHIBIT 3
 
                              AMENDED AND RESTATED
                          CERTIFICATE OF INCORPORATION
                                       OF
                               VISX, INCORPORATED
                            ------------------------
 
    VISX,  INCORPORATED (the  "Company"), a  corporation organized  and existing
under and by virtue of the General Corporation Law of the State of Delaware (the
"General  Corporation   Law"),  having   filed  its   original  Certificate   of
Incorporation  on June 7,  1988, under the  name of TTI  Acquisition Corp., DOES
HEREBY   CERTIFY:   That   the   amendment  and  restatement  of  the  Company's
Certificate  of  Incorporation  was  duly  approved  by  the Company's  Board of
Directors,  and  by  a  majority  of  the  Company's Stockholders, in accordance
with  the  provisions of  Sections 242 and 245 of the General Corporation Law of
the  State  of  Delaware.   Pursuant  to  Sections 242  and 245  of the  General
Corporation  Law,  this  Restated  Certificate  of  Incorporation  restates  and
integrates   and  further  amends   the   provisions   of  the   Certificate  of
Incorporation  of  the  Company.   The  text  of  the  Company's  Certificate of
Incorporation  as  heretofore  amended or  supplemented  is  hereby  amended and
restated in its entirety to read as follows:

         I: The name of the Company is VISX, Incorporated.
 
        II: The address  of its registered  office in the  State of Delaware  is
    1209  Orange  Street, City  of Wilmington,  County  of New  Castle, Delaware
    19801. The name of the registered agent at such address is The Corporation 
    Trust Company.
 
        III: The nature of the business or purposes to be conducted or  promoted
    is  to engage in  any lawful act  or activity for  which corporations may be
    organized under the General Corporation Law of Delaware.
 
        IV:  The  total number  of shares  of all  classes of  stock that  the
       Company  is  authorized  to  issue  is  ninety million (90,000,000) 
       shares of Common Stock with a par value of $0.01 per share.
 
         V: The Company 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  and powers  conferred
    herein   upon  stockholders  and  directors  are  granted  subject  to  this
    reservation.
 
        VI: In furtherance  and not  in limitation  of the  powers conferred  by
    statute,  the Board of Directors is  expressly authorized to adopt, alter or
    repeal the Bylaws of the Company.
 
       VII: Meetings of  stockholders shall  be held  at such  place, within  or
    without  the State  of Delaware, as  may be  designated by or  in the manner
    provided in the Bylaws, or, if  not so designated, at the registered  office
    of  the Company in the State of Delaware. Elections of directors need not be
    by written ballot unless and to the extent that the Bylaws so provide.
 
      VIII: To the fullest extent permitted by the Delaware General  Corporation
    Law  as the  same exists  or may  hereafter be  amended, a  director of this
    Company shall not be liable to the Company or its stockholders for  monetary
    damages  for breach  of fiduciary duty  as a director.  Without limiting the
    foregoing in any respect, a director of this Company shall not be personally
    liable to the Company or its stockholders for monetary damages for breach of
    fiduciary duty as a director,
 
 
<PAGE>

    except for liability (1) for any breach of the director's duty of loyalty to
    the Company or its stockholders, (2) for acts or omissions not in good faith
    or which involve intentional misconduct or  a knowing violation of law,  (3)
    under  Section 174 of the  Delaware General Corporation Law,  or (4) for any
    transaction from which the director derived an improper personal benefit.
 
        IX: (A) RIGHT TO INDEMNIFICATION.
 
               (1) Each person who was or is made a party or is threatened to be
           made a party  to or is  involved in any  action, suit or  proceeding,
           whether    civil,    criminal,   administrative    or   investigative
           (hereinafter, a "proceeding"), by reason of the fact that he or  she,
           or  a person of whom he or she is the legal representative, is or was
           a director or officer of the Company, including service with  respect
           to  employee benefit plans,  whether the basis  of such proceeding is
           alleged action  in  an  official capacity  as  a  director,  officer,
           employee  or  agent  or in  any  other  capacity while  serving  as a
           director, officer , employee or agent, shall be indemnified and  held
           harmless  by  the Company  to the  fullest  extent authorized  by the
           Delaware General Corporation Law, as the same exists or may hereafter
           be amended  (but, in  the case  of any  such amendment,  only to  the
           extent  that such  amendment permits  the Company  to provide broader
           indemnification rights than said law permitted the Company to provide
           prior to such  amendment), against all  expenses, liability and  loss
           (including  attorneys' fees, judgments, fines,  ERISA excise taxes or
           penalties and amounts paid  or to be  paid in settlement)  reasonably
           incurred  or suffered by such person in connection therewith and such
           indemnification shall continue as to a person who has ceased to be  a
           director,  officer, employee or agent and  shall inure to the benefit
           of his or her heirs, executors and administrators.
 
               (2) The Company shall indemnify and hold harmless in such  manner
           any  person who was or is made a  party or is threatened to be made a
           party to a proceeding by reason of the fact that he, she or a  person
           of  whom he or she is the  legal representative, is or was serving at
           the request of the Company as a director, officer, employee or  agent
           of  another  corporation or  a partnership,  joint venture,  trust or
           other enterprise;
 
               (3)  Notwithstanding  the  foregoing,   except  as  provided   in
           paragraph  IX(B) below, the  Company shall indemnify  any such person
           seeking indemnification  in connection  with  a proceeding  (or  part
           thereof)  initiated by such  person only if  such proceeding (or part
           thereof) was authorized by the Board of Directors of the Company.  In
           the  event a  director or  officer of  the Company  shall serve  as a
           director, officer, employee or agent of any corporation, partnership,
           joint venture,  trust  or  other  enterprise  in  which  the  Company
           maintains  an  investment  it  shall  be  conclusively  presumed  for
           purposes of  the indemnification  provided for  in subsection  (A)(2)
           above  that such  service has been  undertaken at the  request of the
           Company. The foregoing presumption shall apply regardless of  whether
           such  director or officer is serving such  entity at the request of a
           third party or that his or her service with such entity was commenced
           prior to  the effectiveness  of this  Article of  the Certificate  of
           Incorporation  or prior to his or her becoming an officer or director
           of the Company. The right to indemnification conferred in  subsection
           (A)(1)  above shall be a contract right  based upon an offer from the
           Company which shall be deemed to be accepted by such person's service
           or continued  service  with the  Company  for any  period  after  the
           adoption  of  this Article  of the  Certificate of  Incorporation and
           shall include  the right  to  be paid  by  the Company  the  expenses
           incurred  in defending  any such proceeding  in advance  of its final
           disposition;  PROVIDED,  HOWEVER,  that  (if  the  Delaware   General
           Corporation  Law requires) the payment of such expenses incurred by a
           director or officer in his or  her capacity as a director or  officer
           (and not in any other capacity in which service was or is rendered by
           such   person  while  a  director   or  officer,  including,  without
           limitation, service to an  employee benefit plan)  in advance of  the
           final disposition of a proceeding shall be made only upon delivery to
           the  Company of an undertaking,  by or on behalf  of such director or
           officer, to repay all


<PAGE>

           amounts so advanced if  it shall ultimately  be determined that  such
           director  or officer  is not  entitled to  be indemnified  under this
           Section or otherwise.  The Company  may, by  action of  its Board  of
           Directors,  provide  indemnification to  employees  or agents  of the
           Company  with   the  same   scope  and   effect  as   the   foregoing
           indemnification of directors and officers.
 
           (B)  RIGHT OF  CLAIMANT TO  BRING SUIT.  If a  claim under subsection
       IX(A)(1) of this Article is not paid in full by the Company within thirty
       days after a written claim has been received by the Company, the claimant
       may at any time thereafter bring suit against the Company to recover  the
       unpaid  amount of the claim, and, if  successful in whole or in part, the
       claimant shall be  entitled to be  paid also the  expense of  prosecuting
       such  claim. It  shall be  a defense  to any  such action  (other than an
       action brought to enforce a claim for expenses incurred in defending  any
       proceeding  in  advance  of  its  final  disposition  where  the required
       undertaking, if any is required, has  been tendered to the Company)  that
       the  claimant  has  not  met  the  standards  of  conduct  which  make it
       permissible under the Delaware General Corporation Law for the Company to
       indemnify the claimant for the amount claimed. Neither the failure of the
       Company (including its Board of Directors, independent legal counsel,  or
       its  stockholders) to have made a determination prior to the commencement
       of such action  that indemnification  of the  claimant is  proper in  the
       circumstances  because  he  or she  has  met the  applicable  standard of
       conduct set forth in the Delaware General Corporation Law, nor an  actual
       determination   by  the  Company  (including   its  Board  of  Directors,
       independent legal counsel, or its stockholders) that the claimant has not
       met such applicable standard of conduct, shall be a defense to the action
       or create a  presumption that  the claimant  has not  met the  applicable
       standard of conduct.
 
           (C)  NON-EXCLUSIVITY OF RIGHTS. The  right to indemnification and the
       payment of expenses incurred in defending a proceeding in advance of  its
       final disposition conferred in this Section shall not be exclusive of any
       other right which any person may have or hereafter acquire under statute,
       provision of the Certificate of Incorporation, by-law, agreement, vote of
       stockholders or disinterested directors, or otherwise.
 
           (D) INSURANCE. The Company may maintain insurance, at its expense, to
       protect  itself  and  any director,  officer,  employee or  agent  of the
       Company or  another corporation,  partnership,  joint venture,  trust  or
       other  enterprise against any such expense, liability or loss, whether or
       not the Company  would have the  power to indemnify  such person  against
       such expense, liability or loss under the Delaware Corporation Law.
 
         X: Whenever a compromise or arrangement is proposed between the Company
    and  its creditors or any  class of them and/or  between the Company 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 the
    Company  or of any creditor or stockholder  thereof or on the application of
    any receiver or receivers appointed for the Company under the provisions  of
    Section  291 Title 8 of the Delaware  Code or on the application of trustees
    in dissolution or any receiver or receivers appointed for the Company  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 the Company, 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 the Company, as  the
    case   may  be,  agree   to  any  compromise  or   arrangement  and  to  any
    reorganization of  this  Company 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 the  Company, as the case  may
    be, and also on the Company.
 

<PAGE>

    RESOLVED  FURTHER, that  the foregoing  Amended and  Restated Certificate of
Incorporation is hereby approved and adopted.
 
    IN WITNESS WHEREOF, VISX, INCORPORATED has caused this Restated  Certificate
to  be signed by Mark B. Logan,  its President and Chief Executive Officer, this
20th day of September  , 1996.
 
                                          VISX, INCORPORATED
 
                                          By: /s/ Mark B. Logan
                                             -----------------------------------
                                              Mark B. Logan
                                             PRESIDENT AND CHIEF EXECUTIVE
                                              OFFICER