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                                                                 EXHIBIT 3.1
                                                                 -----------

                           CERTIFICATE OF AMENDMENT
                                    OF THE
               AMENDED AND RESTATED CERTIFICATE OF INCORPORATION
                                      OF
                               ALLSCRIPTS, INC.
                  (Incorporated in Delaware on July 13, 1999)
                             * * * * * * * * * * *

     Allscripts, 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 by a meeting held
on April 7, 2000, adopted a resolution proposing and declaring advisable the
following amendment to the Certificate of Incorporation of said corporation:

     RESOLVED, that Section 1 of Article Fourth is hereby deleted in its
     entirety and replaced with the following:

          FOURTH:

                    1.  Authorized Shares. The total number of shares
          of stock of all classes which the Corporation shall have
          authority to issue is one hundred fifty one million
          (151,000,000), of which one million (1,000,000) shall be
          shares of Preferred Stock with a par value of $0.01 per
          share ("Preferred Stock"), and one hundred fifty million
          (150,000,000) shall be shares of Common Stock with a par
          value of $0.01 per share ("Common Stock").

     SECOND: That the stockholders at a meeting held on May 10, 2000 approved
said amendment in accordance with the provisions of Section 242(b) of the
General Corporation Law of the State of Delaware.

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

     IN WITNESS WHEREOF, said corporation has caused this certificate to be
signed by an authorized officer this 18th day of May, 2000.

                                        ALLSCRIPTS, INC.

                                        By: /s/ John Cull
                                            ------------------------------
                                        Its: Secretary and Treasurer
<PAGE>

               AMENDED AND RESTATED CERTIFICATE OF INCORPORATION
                                      OF
                               ALLSCRIPTS, INC.
                  (Incorporated in Delaware on July 13, 1999)


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

     FIRST:  Pursuant to Section 245(b) and 242 of the General Corporation Law
of the State of Delaware (the "Delaware Law"), the Certificate of Incorporation,
as amended, of ALLSCRIPTS, INC., a Delaware corporation (the "Corporation") is
hereby amended and restated to read in its entirety as follows:

              "AMENDED AND RESTATED CERTIFICATE OF INCORPORATION

     FIRST:  The name of the corporation is Allscripts, Inc.

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

     THIRD:  The nature of the business and the objects and purposes to be
conducted or promoted by the Corporation are to engage in any lawful act or
activity for which corporations may be organized under the General Corporation
Law of the State of Delaware.

     FOURTH:

     1.   Authorized Shares.  The total number of shares of stock of all classes
which the Corporation shall have authority to issue is seventy-six million
(76,000,000), of which one million (1,000,000) shall be shares of Preferred
Stock with a par value of $0.01 per share ("Preferred Stock"), and seventy-five
million (75,000,000) shall be shares of Common Stock with a par value of $0.01
per share ("Common Stock").

     2.   Preferred Stock.

     (a)  The Preferred Stock shall be issuable in series, and in connection
with the issuance of any series of Preferred Stock and to the extent now or
hereafter permitted by the laws of the State of Delaware, the Board of Directors
is authorized to fix by resolution the designation of each series, the stated
value of the shares of each series, the dividend rate or rates of each series
(which rate or rates may be expressed in terms of a formula or other method by
which such rate or rates shall be calculated from time to time) and the date or
dates and other provisions respecting the payment of dividends, the provisions,
if any, for a sinking fund for the shares of each series, the preferences of the
shares of each series in the event of the liquidation or dissolution of the
Corporation, the provisions, if any, respecting the redemption of the shares of
each series and, subject to requirements of the laws of the State of Delaware,
the voting rights (except that such shares shall not have more than one vote per
share), the terms, if any, upon which the shares of each series shall be
convertible into or exchangeable for any other shares of stock of the
Corporation and any other relative, participating, optional or other special
rights, and qualifications, limitations or restrictions thereof, of the shares
of each series.

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     (b)  Preferred Stock of any series redeemed, converted, exchanged,
purchased, or otherwise acquired by the Corporation shall constitute authorized
but unissued Preferred Stock.

     (c)  All shares of any series of Preferred Stock, as between themselves,
shall rank equally and be identical (except that such shares may have different
dividend provisions); and all series of Preferred Stock, as between themselves,
shall rank equally and be identical except as set forth in resolutions of the
Board of Directors authorizing the issuance of such series.

     3.   Common Stock.

     (a)  After dividends to which the holders of Preferred Stock may then be
entitled under the resolutions creating any series thereof have been declared
and after the Corporation shall have set apart the amounts required pursuant to
such resolutions for the purchase or redemption of any series of Preferred
Stock, the holders of Common Stock shall be entitled to have dividends declared
in cash, property, or other securities of the Corporation out of any net profits
or net assets of the Corporation legally available therefor, if, as and when
such dividends are declared by the Corporation's Board of Directors.

     (b)  In the event of the liquidation or dissolution of the Corporation's
business and after the holders of Preferred Stock shall have received amounts to
which they are entitled under the resolutions creating such series, the holders
of Common Stock shall be entitled to receive ratably the balance of the
Corporation's net assets available for distribution.

     (c)  Each share of Common Stock shall be entitled to one vote upon all
matters upon which stockholders have the right to vote, but shall not be
entitled to vote for the election of any directors who may be elected by vote of
the Preferred Stock voting as a class if so provided in the resolution creating
such Preferred Stock pursuant to Section 2(a) of this Article FOURTH.

     4.   Preemptive Rights.  No holder of any shares of the Corporation shall
have any preemptive right to subscribe for or to acquire any additional shares
of the Corporation of the same or of any other class whether now or hereafter
authorized or any options or warrants giving the right to purchase any such
shares, or any bonds, notes, debentures or other obligations convertible into
any such shares.

     FIFTH:  The Corporation is to have perpetual existence.

     SIXTH:  The private property of the stockholders shall not be subject to
the payment of corporate debts to any extent whatever.

     SEVENTH:  Except as may otherwise be fixed by resolution of the Board of
Directors pursuant to the provisions of Article FOURTH hereof relating to the
rights of the holders of Preferred Stock to elect directors as a class, the
number of directors of the Corporation shall be fixed from time to time by or
pursuant to the By-Laws of the Corporation. The directors, other than those who
may be elected by the holders of Preferred Stock, shall be classified, with
respect to the time for which they severally hold office, into three classes, as
nearly equal in number as possible. The first class shall be initially elected
for a term expiring at the next ensuing annual meeting, the second class shall
be initially elected for a term expiring one year thereafter, and the third
class shall be elected for a term expiring two years thereafter, with each
member of each class to hold office until his successor is elected and
qualified. At each annual meeting of the stockholders of the Corporation held
after the initial classification and
<PAGE>

election of directors, the successors of the class of directors whose term
expires at that meeting shall be elected to hold office for a term expiring at
the annual meeting of stockholders held in the third year following the year of
their election.

     Advance notice of stockholder nominations for the election of directors
shall be given in the manner provided in the By-Laws of the Corporation.

     Except as may otherwise be fixed by resolution of the Board of Directors
pursuant to the provisions of Article FOURTH hereof relating to the rights of
the holders of Preferred Stock to elect directors as a class, newly created
directorships resulting from any increase in the number of directors and any
vacancies on the Board of Directors resulting from death, resignation,
disqualification, removal or any other cause shall be filled by the affirmative
vote of a majority of the remaining directors then in office, even though less
than a quorum of the Board of Directors. Any director elected in accordance with
the preceding sentence shall hold office for the remainder of the full term of
the class of directors in which the new directorship was created (subject to the
requirements of this Article SEVENTH that all classes be as nearly equal in
number as possible) or in which the vacancy occurred and until such director's
successor shall have been elected and qualified. No decrease in the number of
directors constituting the Board of Directors shall shorten the term of an
incumbent director.

     Subject to any rights of the holders of Preferred Stock to elect directors
as a class, a director may be removed only for cause and only by the affirmative
vote of the holders of 80% of the combined voting power of the then outstanding
shares of stock entitled to vote generally in the election of directors, voting
together as a single class.

     In furtherance and not in limitation of the powers conferred by statute,
the Board of Directors is expressly authorized:

          1.   To adopt, amend and repeal the By-Laws of the Corporation. Any
     By-Laws adopted by the directors under the powers conferred hereby may be
     amended or repealed by the directors or by the stockholders.
     Notwithstanding the foregoing or any other provision in this Certificate of
     Incorporation or the By-Laws of the Corporation to the contrary, Article
     II, Sections 3 and 7 and Article III, Sections 1, 2 and 3 of the By-Laws
     shall not be amended or repealed and no provision inconsistent therewith
     shall be adopted without the affirmative vote of the holders of at least
     80% of the voting power of all the shares of the Corporation entitled to
     vote generally in the election of directors, voting together as a single
     class.

          2.   To fix and determine, and to vary the amount of, the working
     capital of the Corporation, and to determine the use or investment of any
     assets of the Corporation, to set apart out of any of the funds of the
     Corporation available for dividends a reserve or reserves for any proper
     purpose and to abolish any such reserve or reserves.

          3.   To authorize the purchase or other acquisition of shares of stock
     of the Corporation or any of its bonds, debentures, notes, scrip, warrants
     or other securities or evidence of indebtedness.

          4.   Except as otherwise provided by law, to determine the places
     within or without the State of Delaware, where any or all of the books of
     the Corporation shall be kept.
<PAGE>

          5.   To authorize the sale, lease or other disposition of any part or
     parts of the properties of the Corporation and to cease to conduct the
     business connected therewith or again to resume the same, as it may deem
     best.

          6.   To authorize the borrowing of money, the issuance of bonds,
     debentures and other obligations or evidences of indebtedness of the
     Corporation, secured or unsecured, and the inclusion of provisions as to
     redeemability and convertibility into shares of stock of the Corporation or
     otherwise; and the mortgaging or pledging, as security for money borrowed
     or bonds, notes, debentures or other obligations issued by the Corporation,
     of any property of the Corporation, real or personal, then owned or
     thereafter acquired by the Corporation.

          7.   To authorize the negotiation and execution on behalf of the
     Corporation of agreements with officers and other employees of the
     corporation relating to the payment of severance compensation to such
     officers or employees.

     In addition to the powers and authorities herein or by statute expressly
conferred upon it, the Board of Directors may exercise all such powers and do
all such acts and things as may be exercised or done by the Corporation,
subject, nevertheless, to the provisions of the laws of the State of Delaware,
of this Certificate of Incorporation and of the By-Laws of the Corporation.

     Subject to any limitation in the By-Laws, the members of the Board of
Directors shall be entitled to reasonable fees, salaries, or other compensation
for their services, as determined from time to time by the Board of Directors,
and to reimbursement for their expenses as such members. Nothing herein
contained shall preclude any director from serving the Corporation or its
subsidiaries or affiliates in any other capacity and receiving compensation
therefor.

     Notwithstanding anything contained in this Amended and Restated Certificate
of Incorporation to the contrary, the affirmative vote of the holders of at
least 80% of the voting power of all shares of the Corporation entitled to vote
generally in the election of directors, voting together as a single class, shall
be required to alter, amend, adopt any provision inconsistent with or repeal
this Article SEVENTH.

     EIGHTH:  Both stockholders and directors shall have power, if the By-Laws
so provide, to hold their meetings and to have one or more offices within or
without the State of Delaware.

     Except as may otherwise be fixed by resolution of the Board of Directors
pursuant to the provisions of Article FOURTH hereof relating to the rights of
the holders of Preferred Stock, any action required or permitted to be taken by
the stockholders of the Corporation may be effected at a duly called annual or
special meeting of such holders and may not be effected by any consent in
writing by such holders. Except as otherwise required by law and subject to the
rights of the holders of Preferred Stock, special meetings of stockholders may
be called only by the Chairman, if any, on his own initiative, the President on
his own initiative or by the Board of Directors pursuant to a resolution
approved by a majority of the entire Board of Directors. Notwithstanding
anything contained in this Amended and Restated Certificate of Incorporation to
the contrary, the affirmative vote of the holders of at least 80% of the voting
power of all shares of the Corporation entitled to vote generally in the
election of directors, voting together as a single class, shall be required to
alter, amend, adopt any provision inconsistent with or repeal this Article
EIGHTH.

     NINTH:  Except as otherwise provided in this Amended and Restated
Certificate of Incorporation, the Corporation reserves the right to amend,
alter, change or repeal any provision contained in this Amended and Restated
Certificate of Incorporation in the manner now or hereafter
<PAGE>

prescribed by statute, and all rights conferred upon stockholders herein are
granted subject to this reservation.

     TENTH:

     (a)  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 General  Corporation Law of the
State of Delaware, or (iv) for any transaction from which the director derived
an improper personal benefit.  If the General Corporation Law of the State of
Delaware, or any other applicable law, is amended 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 General Corporation Law of the State of
Delaware, or any other applicable law, as so amended.  Any repeal or
modification of this Section (a) by the stockholders of the Corporation shall
not adversely affect any right or protection of a director of the Corporation
existing at the time of such repeal or modification.

     (b)  (1)  Each person who has 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 Corporation or is or was
serving at the request of the Corporation as a director, officer or employee or
agent of another corporation or of a partnership, joint venture, trust or other
enterprise, including service with respect to employee benefit plans, whether
the basis of such proceeding is an 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 Corporation to the fullest extent authorized by the General Corporation Law
of the State of Delaware, or any other applicable 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 Corporation to provide broader indemnification
rights than said law permitted the Corporation 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; provided, however, that except
as provided in paragraph (2) of this Section (b) with respect to proceedings
seeking to enforce rights to indemnification, the Corporation 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 Corporation.  The right to
indemnification conferred in this Section (b) shall be a contract right and
shall include the right to be paid by the Corporation the expenses incurred in
defending any such proceeding in advance of its final disposition; provided,
however, that if the General Corporation Law of the State of Delaware, or any
other applicable 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 Corporation of an undertaking by or on behalf of such
director or officer to repay all amounts so advanced if it shall ultimately be
determined that such director or officer is not entitled to be indemnified under
this Section (b) or otherwise.
<PAGE>

     (2)  If a claim under paragraph (1) of this Section (b) is not paid in full
by the Corporation within thirty days after a written claim has been received by
the Corporation, the claimant may at any time thereafter bring suit against the
Corporation 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 Corporation) that the claimant has
not met the standard of conduct which make it permissible under the General
Corporation Law of the State of Delaware, or any other applicable law, for the
Corporation to indemnify the claimant for the amount claimed, but the burden of
proving such defense shall be on the Corporation. Neither the failure of the
Corporation (including its Board of Directors, stockholders or independent legal
counsel) 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 General
Corporation Law of the State of Delaware, or any other applicable law, nor an
actual determination by the Corporation (including its Board of Directors,
stockholders or independent legal counsel) 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.

     (3)  The right to indemnification and the payment of expenses incurred in
defending a proceeding in advance of its final disposition conferred in this
Section (b) shall not be exclusive of any other right which any person may have
or hereafter acquire under any statute, provision of this Certificate of
Incorporation, By-Law, agreement, vote of stockholders or disinterested
directors or otherwise.

     (4)  The Corporation may maintain insurance, at its expense, to protect
itself and any director, officer, employee or agent of the Corporation or
another corporation, partnership, joint venture, trust or other enterprise
against any expense, liability or loss, whether or not the Corporation would
have the power to indemnify such person against such expense, liability or loss
under the General Corporation Law of the State of Delaware, or any other
applicable law.

     (5)  The Corporation may, to the extent authorized from time to time by the
Board of Directors, grant rights to indemnification, and rights to be paid by
the Corporation the expenses incurred in defending any proceeding in advance of
its final disposition, to any employee or agent of the Corporation to the
fullest extent of the provisions of this Section (b) with respect to the
indemnification and advancement of expenses of directors and officers of the
Corporation.

     (6)  Any repeal or modification of this Section (b) by the stockholders of
the Corporation shall not adversely affect any right or protection of a
director, officer, employee or agent of the Corporation existing at the time of
such repeal or modification.

     ELEVENTH:  In determining whether an "Acquisition Proposal" is in the best
interests of the Corporation and its stockholders, the Board of Directors may,
to the extent permitted by law, consider all factors it deems relevant
including, without limitation, the following:

     (a)  The consideration being offered in the Acquisition Proposal, not only
in relation to the then current market price, but also in relation to the then
current value of the Corporation in a freely negotiated transaction and in
relation to the Board of Directors' estimate of the future value of the
Corporation as an independent entity; and
<PAGE>

     (b)  Such other factors the Board of Directors determines to be relevant,
including among others the social, legal and economic effects upon employees,
suppliers, customers and the communities in which the Corporation is located, as
well as on the long term business prospects of the Corporation.

     "Acquisition Proposal" means any proposal of any person (i) for a tender
offer, exchange offer or any other method of acquiring any equity securities of
the Corporation with a view to acquiring control of the Corporation, (ii) to
merge or consolidate the Corporation with another corporation, or (iii) to
purchase or otherwise acquire all or substantially all of the properties and
assets of the Corporation.

     This Article ELEVENTH shall not be interpreted to create any rights on
behalf of third persons, such as employees, suppliers, or customers.

     TWELFTH:  The Corporation has elected to be governed by Section 203 of the
General Corporation Law of Delaware."

     SECOND:  The Board of Directors of the Corporation, by unanimous written
consent, duly adopted resolutions proposing and approving the Amended and
Restated Certificate of Incorporation of the Corporation and directing that such
Amended and Restated Certificate of Incorporation be submitted to the
stockholder of the Corporation to consider and adopt the same.

     THIRD:  Pursuant to Section 211 of the Delaware Law, the adoption of the
Amended and Restated Certificate of Incorporation was consented to at a meeting
by the holder of the voting power of all shares of capital stock of the
Corporation entitled to vote thereon.

     FOURTH:  The Amended and Restated Certificate of Incorporation was duly
adopted in accordance with the provisions of the General Corporation Law of the
State of Delaware.

     IN WITNESS WHEREOF, ALLSCRIPTS, INC. has caused this Certificate to be
signed by its Secretary and Treasurer this 21st day of July, 1999.

                                              ALLSCRIPTS, INC.


                                              By: /s/  John G. Cull
                                                  ---------------------------
                                                  John G. Cull,
                                                  Secretary and Treasurer