<PAGE>
 
                                                                     EXHIBIT 3.4


                     RESTATED CERTIFICATE OF INCORPORATION

                                       OF

                         CALYPTE BIOMEDICAL CORPORATION

     The following Restated Certificate of Incorporation of Calypte Biomedical
Corporation (i) restates the provisions of the Certificate of Incorporation of
Calypte Biomedical Corporation filed with the Secretary of State of the State of
Delaware on June 11, 1996, and (ii) supersedes the original Certificate of
Incorporation and all prior restatements thereof and amendments thereto in their
entirety.

                                   ARTICLE I

     The name of the corporation is Calypte Biomedical Corporation. (the
"Corporation").


                                   ARTICLE II

     The address of the Corporation's registered office in the State of Delaware
is 1209 Orange Street, City of Wilmington, County of New Castle, Delaware 19801.
The name of its registered agent at such address is The Corporation Trust
Company.


                                  ARTICLE III

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


                                   ARTICLE IV

     The Corporation is authorized to issue two classes of shares of stock to be
designated, respectively, Common Stock, $0.001 par value, and Preferred Stock,
$0.001 par value.  The total number of shares that the Corporation is authorized
to issue is 25,000,000 shares.  The number of shares of Common Stock authorized
is 20,000,000.  The number of shares of Preferred authorized is 5,000,000.

     The Preferred Stock may be issued from time to time in one or more series
pursuant to a resolution or resolutions providing for such issue duly adopted by
the board of directors (authority to do so being hereby expressly vested in the
board).  The board of directors is further authorized to determine or alter the
rights, preferences, privileges and restrictions granted to or imposed upon any
wholly unissued series of Preferred Stock and to fix the number of shares of any
series of Preferred Stock and the designation of any such series of Preferred
Stock.  The board of directors, within the limits and restrictions stated in any
resolution or resolutions of the board of directors originally fixing the number


<PAGE>
 
of shares constituting any series, may increase or decrease (but not below the
number of shares in any such series then outstanding) the number of shares of
any series subsequent to the issue of shares of that series.

     The authority of the board of directors with respect to each such class or
series shall include, without limitation of the foregoing, the right to
determine and fix:

     (a) the distinctive designation of such class or series and the number of
shares to constitute such class or series;

     (b) the rate at which dividends on the shares of such class or series shall
be declared and paid, or set aside for payment, whether dividends at the rate so
determined shall be cumulative or accruing, and whether the shares of such class
or series shall be entitled to any participating or other dividends in addition
to dividends at the rate so determined, and if so, on what terms;

     (c) the right or obligation, if any, of the corporation to redeem shares of
the particular class or series of Preferred Stock and, if redeemable, the price,
terms and manner of such redemption;

     (d) the special and relative rights and preferences, if any, and the amount
or amounts per share, which the shares of such class or series of Preferred
Stock shall be entitled to receive upon any voluntary of involuntary
liquidation, dissolution or winding up of the Corporation;

     (e) the terms and conditions, if any, upon which shares of such class or
series shall be convertible into, or exchangeable for, shares of capital stock
of any other class or series, including the price or prices or the rate or rates
of conversion or exchange and the terms of adjustment, if any.

     (f) the obligation, if any, of the corporation to retire, redeem or
purchase shares of such class or series pursuant to a sinking fund or fund of a
similar nature or otherwise, and the terms and conditions of such obligation;
 
     (g) voting rights, if any, on the issuance of additional shares of such
class or series or any shares of any other class of series of Preferred Stock;

     (h) limitations, if any, on the issuance of additional shares of such class
or series or any shares of any other class or series of Preferred Stock; and

     (i) such other preferences, powers, qualifications, special or relative
rights and privileges thereof as the board of directors of the corporation,
acting in accordance with this Restated Certificate of Incorporation, may deem
advisable and are not inconsistent with law and the provisions of this Restated
Certificate of Incorporation.

                                      -2-
<PAGE>
 
                                   ARTICLE V

     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 upon the stockholders
herein are granted subject to this right.


                                   ARTICLE VI

     The Corporation is to have perpetual existence.


                                  ARTICLE VII

     1.  Limitation of Liability.  To the fullest extent permitted by the
         -----------------------                                         
General Corporation Law of the State of Delaware as the same exists or as may
hereafter be amended, 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.

     2.  Indemnification.  The Corporation may indemnify to the fullest extent
         ---------------                                                      
permitted by law any person made or threatened to be made a party to an action
or proceeding, whether criminal, civil, administrative or investigative, by
reason of the fact that such person or his or her testator or intestate is or
was a director, officer or employee of the Corporation, or any predecessor of
the Corporation, or serves or served at any other enterprise as a director,
officer or employee at the request of the Corporation or any predecessor to the
Corporation.

     3.  Amendments.  Neither any amendment nor repeal of this Article VII, nor
         ----------                                                            
the adoption of any provision of the Corporation's Certificate of Incorporation
inconsistent with this Article VII, shall eliminate or reduce the effect of this
Article VII, in respect of any matter occurring, or any action or proceeding
accruing or arising or that, but for this Article VII, would accrue or arise,
prior to such amendment, repeal, or adoption of an inconsistent provision.


                                  ARTICLE VIII

     In the event any shares of Preferred Stock shall be redeemed or converted
pursuant to the terms hereof, the shares so converted or redeemed shall not
revert to the status of authorized but unissued shares, but instead shall be
canceled and shall not be re-issuable by the Corporation.

                                      -3-
<PAGE>
 
                                   ARTICLE IX

     Holders of stock of any class or series of this corporation shall not be
entitled to cumulate their votes for the election of directors of any other
matter submitted to a vote of the stockholders, unless such cumulative voting is
required pursuant to Sections 2115 and/or 301.5 of the California Corporations
Code, in which event each such holder shall be entitled to as many votes as
shall equal the number of votes which (except for this provision as to
cumulative voting) such holder would be entitled to cast for the election of
directors with respect to his shares of stock multiplied by the number of
directors to be elected by him, and the holder may cast all of such votes for a
single director or may distribute them among the number of directors to be voted
for, or for any two or more of them as such holder may see fit, so long as the
name of the candidate for director shall have been placed in nomination prior to
the voting and the stockholder, or any other holder of the same class or series
of stock, has given notice at the meeting prior to the voting of the intention
to cumulate votes.


                                   ARTICLE X

     1.  Number of Directors.  The number of directors which constitutes the
         -------------------                                                
whole Board of Directors of the corporation shall be designated in the Bylaws of
the corporation.

     2.  Election of Directors.  Elections of directors need not be by written
         ---------------------                                                
ballot unless the Bylaws of the corporation shall so provide.


                                   ARTICLE XI

     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 XII

     Immediately upon the closing of a public offering pursuant to an effective
registration statement under the Securities Act of 1933, as amended, covering
any of the corporation's securities (as that term is defined under the
Securities Act of 1933, as then in effect), no action shall be taken by the
stockholders of the corporation except at an annual or special meeting of the
stockholders called in accordance with the Bylaws of the corporation and no
action shall be taken by the stockholders by written consent.


                                  ARTICLE XIII

     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 of 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.

                                      -4-
<PAGE>
 
     This Restated Certificate of Incorporation has been duly adopted by the
board of directors of the Corporation in accordance with the provisions of
Sections 242 and 245 of the General Corporation Law of the State of Delaware, as
amended.

     This Restated Certificate of Incorporation has been duly approved by the
shareholders of the Corporation in accordance with the provisions of Section 228
of the General Corporation Law of the State of Delaware, as amended.

     IN WITNESS WHEREOF, Calypte Biomedical Corporation has caused this
certificate to be signed by John P. Davis, its President and Chief Executive
Officer, and John J. DiPietro, its Secretary, this 31st day of July, 1996.



                              By:  /s/ John P. Davis
                                   --------------------------------------------
                                   John P. Davis, President and Chief Executive
                                   Officer


ATTEST:

/s/ John J. DiPietro
---------------------------
John J. DiPietro, Secretary

                                      -5-