<PAGE>
 
                                                                   EXHIBIT 10(E)
                                                                                

                                AMENDMENT NO. 2
                                      TO
                        AMERICAN DENTAL PARTNERS, INC.
                  AMENDED AND RESTATED 1996 STOCK OPTION PLAN
                  -------------------------------------------

     The American Dental Partners, Inc. Amended and Restated 1996 Stock Option
Plan, as previously amended (the "Plan"), is hereby amended pursuant to the
following provisions:

     1.   Definitions
          -----------

     All capitalized terms used in this amendment which are not otherwise
defined herein shall have the respective meanings given such terms in the Plan.

     2.   Manner of Exercise
          ------------------

     Section 8(b) of the Plan is hereby deleted from the Plan in its entirety
and replaced with the following:

          (b)  To the extent that the right to purchase shares under an option
     has accrued and is in effect, options may be exercised in full at one time
     or in part from time to time, by giving written notice, signed by the
     person or persons exercising the option, to the Company, stating the number
     of shares with respect to which the option is being exercised, accompanied
     by payment in full for such shares as provided in subparagraph (a) above.
     Upon such exercise, delivery of a certificate for paid-up non-assessable
     shares shall be made at the principal office of the Company to the person
     or persons exercising the option at such time, during ordinary business
     hours, not more than thirty (30) days from the date of receipt of the
     notice by the Company, as shall be designated in such notice, or at such
     time, place and manner as may be agreed upon by the Company and the person
     or persons exercising the option. Upon exercise of the option and payment
     as provided above, the optionee shall become a shareholder of the Company
     as to the shares acquired upon such exercise.

     3.   Change in Control
          -----------------

     Section 13 of the Plan is hereby deleted from the Plan in its entirety and
replaced with the following:

     13.  Change in Control.
          ----------------- 

          (a)  Accelerated Vesting and Company Purchase Option. Notwithstanding
               -----------------------------------------------   
     any provision of the Plan or any Agreement to the contrary (unless such
     Agreement contains a provision referring specifically to this Section 13
     and stating that this Section 13 shall not be applicable to the option
     evidenced by such Agreement), if a Change in Control (as defined below)
     occurs, then:
<PAGE>
 
          (i)  Any and all options theretofore granted under the Plan and not
     fully vested shall thereupon become vested and exercisable in full and
     shall remain so exercisable in accordance with their terms; provided that
     no option which has previously been exercised or otherwise terminated shall
     become exercisable; and

          (ii) The Company may, at its option, terminate any or all unexercised
     options and portions thereof not more than 30 days after such Change in
     Control; provided that the Company shall, upon such termination and with
     respect to each option so terminated, pay to the optionee (or such
     optionee's transferee, if applicable) theretofore holding such option cash
     in an amount equal to the difference between the fair market value (as
     defined in Section 7, above) of the shares of Common Stock subject to the
     option at the time the Company exercises its option under this Section
     13(a)(ii) and the exercise price of the option, less applicable withholding
     taxes; and provided further that if such fair market value is less than
     such exercise price, then the Board may, in its sole discretion, terminate
     such option without any payment.

     (b)  Definition of Change in Control. For purposes of the Plan, a "Change 
          -------------------------------    
in Control" shall mean the happening of any of the following:

          (i)  The direct or indirect acquisition by any "person" as defined in
     (S)3(a)(9) of the 1934 Act and as used in (S)(S)13(d) and 14(d) thereof,
     including a "group" within the meaning of (S)13(d) of the 1934 Act
     (hereinafter, simply a "Person"), of "beneficial ownership" (within the
     meaning of Rule 13d-3 under the 1934 Act) of securities of the Company
     representing more than 50% of the combined voting power of the Company's
     then outstanding voting securities entitled to vote generally in the
     election of directors of the Company (the "Company Voting Securities");
     provided that: (A) for purposes of this subsection (i), the term "Person"
     shall not include the Company, any subsidiary of the Company, any employee
     benefit plan sponsored or maintained by the Company or any subsidiary of
     the Company (including any trustee of such plan acting as trustee), any
     person who was a stockholder of the Company on the effective date of the
     Plan (an "Existing Stockholder"), and any affiliate of an Existing
     Stockholder; and (B) the provisions of this subsection (i) shall not apply
     to (1) any acquisition of securities from the Company or any of its
     subsidiaries, or (2) any acquisition of securities pursuant to a Business
     Combination (as defined below) which satisfies clauses (A), (B), and (C) of
     subsection (iii) of this Section 13(b);

          (ii) When, during any period of 24 consecutive months during the
     existence of the Plan, the individuals who, at the beginning of such period
     constitute the Board (the "Incumbent Directors") cease for any reason other
     than death to constitute at least at least a majority of the Board;
     provided, however, that a director who was not a director at the beginning
     of such 24-month period shall be deemed to have satisfied such 24-month
     requirement (and be an

                                      -2-
<PAGE>
 
          Incumbent Director) if such director was elected by, or on the
          recommendation of or with the approval of, at least two-thirds of the
          directors who then qualified as Incumbent Directors either actually
          (because they were directors at the beginning of such 24-month period)
          or by prior operation of this Section 13 (b)(ii); or

               (iii) Approval by the stockholders of the Company of a
          reorganization, merger, consolidation, or recapitalization of the
          Company, or a sale or other disposition of all or substantially all of
          the assets of the Company, or the acquisition of the assets of another
          corporation (any such transaction, a "Business Combination"), or the
          consummation of a Business Combination for which stockholder approval
          is not obtained, unless, in any such case, following such Business
          Combination: (A) all or substantially all of the individuals and
          entities who were the beneficial owners of the Company Voting
          Securities outstanding immediately prior to such Business Combination
          beneficially own, directly or indirectly, immediately following such
          Business Combination, more than 50% of the combined voting power of
          the then outstanding voting securities entitled to vote generally in
          the election of directors of the corporation resulting from such
          Business Combination in substantially the same proportions as their
          ownership of the Company Voting Securities immediately prior to such
          Business Combination, and (B) at least a majority of the members of
          the board of directors of the corporation resulting from such Business
          Combination were Incumbent Directors at the time of the execution of
          the initial agreement, or of the action of the Board, providing for
          such Business Combination; or

               (iv)  Approval by the stockholders of the Company of a complete
          liquidation or dissolution of the Company.

          4.   Effective Date; Construction
               ----------------------------

     The effective date of this amendment is November 6, 1998, and this
amendment shall be deemed to be a part of the Plan as of such date and shall be
applicable to all options granted under the Plan prior to that date, as well as
options hereafter granted under the Plan.  In the event of any inconsistencies
between the provisions of the Plan and this amendment, the provisions of this
amendment shall control.  Except as modified by this amendment, the Plan shall
continue in full force and effect without change.

                                      -3-
<PAGE>
 
                                                                   EXHIBIT 10(E)
                                                                                

                                AMENDMENT NO. 3
                                      TO
                        AMERICAN DENTAL PARTNERS, INC.
                  AMENDED AND RESTATED 1996 STOCK OPTION PLAN
                  -------------------------------------------

     The American Dental Partners, Inc. Amended and Restated 1996 Stock Option
Plan, as previously amended by Amendment No. 1 dated February 27, 1998
("Amendment No. 1") and Amendment No. 2 dated November 6, 1998 (collectively,
the "Plan"), is hereby amended pursuant to the following provisions:

     1.  Definitions
         -----------

     All capitalized terms used in this amendment which are not otherwise
defined herein shall have the respective meanings given such terms in the Plan.

     2.  Shares Subject To Plan
         ----------------------

     The total number of shares of Common Stock for which options may be granted
under the Plan, as provided under Section 2(a) of the Plan, as previously
adjusted pursuant to Section 12 of the Plan and increased by Amendment No. 1, is
increased by 300,000 shares to a total of 1,273,246 shares of Common Stock.

     3.  Effective Date; Construction
         ----------------------------

     The effective date of this amendment is February 26, 1999, and this
amendment shall be deemed to be a part of the Plan as of such date.  In the
event of any inconsistencies between the provisions of the Plan and this
amendment, the provisions of this amendment shall control.  Except as modified
by this amendment, the Plan shall continue in full force and effect without
change.

     This amendment shall be submitted to the stockholders of the Company for
approval as soon as reasonably practicable, but in any event not later than 12
months after the date of this amendment.  Notwithstanding the preceding
paragraph or any other provisions of this amendment to the contrary, if this
amendment is not approved by the stockholders of the Company within such 12-
month period, this amendment and all options granted with respect to the
additional shares of Common Stock subject to the Plan as a result of this
amendment shall automatically become null and void and have no further force or
effect.