ALLSCRIPTS HEALTHCARE SOLUTIONS, INC. 3.50% CONVERTIBLE SENIOR DEBENTURES DUE 2024 Resale Registration Rights Agreement

Exhibit 4.2

EXECUTION COPY

BANC OF AMERICA SECURITIES LLC

$75,000,000 AGGREGATE PRINCIPAL AMOUNT

ALLSCRIPTS HEALTHCARE SOLUTIONS, INC.

3.50% CONVERTIBLE SENIOR DEBENTURES

DUE 2024

Resale Registration Rights Agreement

dated July 6, 2004

1

RESALE REGISTRATION RIGHTS AGREEMENT, dated as of July 6, 2004, between Allscripts Healthcare Solutions, Inc., a Delaware corporation (together with any successor entity, the “ Company ”) and Banc of America Securities LLC, as representative of the several initial purchasers (the “ Initial Purchasers ”) under the Purchase Agreement (as defined below).

Pursuant to the Purchase Agreement, dated as of June 29, 2004, between the Company and Banc of America Securities LLC, as representative of the Initial Purchasers (the “ Purchase Agreement ”), the Initial Purchasers have agreed to purchase from the Company $75,000,000 ($82,500,000 if the Initial Purchasers exercise their option in full) in aggregate principal amount of the Company’s 3.50% Convertible Senior Debentures due 2024 (the “ Debentures ”). The Debentures will be convertible into fully paid, nonassessable shares of common stock, par value $0.01 per share, of the Company (“ Common Stock ”), cash or a combination of shares of Common Stock and cash, at the Company’s option. The Debentures will be convertible on the terms, and subject to the conditions, set forth in the Indenture (as defined herein). To induce the Initial Purchasers to purchase the Debentures, the Company has agreed to provide the registration rights set forth in this Agreement pursuant to Section 5(g) of the Purchase Agreement.

The parties hereby agree as follows:

1. Definitions. Capitalized terms used in this Agreement without definition shall have their respective meanings set forth in the Purchase Agreement. As used in this Agreement, the following capitalized terms shall have the following meanings:

“ Affiliate ” of any specified Person means any other Person that, directly or indirectly, is in control of, is controlled by, or is under common control with, such specified Person. For purposes of this definition, control of a Person means the power, direct or indirect, to direct or cause the direction of the management and policies of such Person whether by contract or otherwise, and the terms “controlling” and “controlled” have meanings correlative to the foregoing.

“ Agreement ” means this Resale Registration Rights Agreement, as amended from time to time in accordance with the terms hereof.

“ Amended Effectiveness Deadline Date ” has the meaning set forth in Section 2(e) hereof.

“ Business Day ” has the meaning set forth in the Indenture.

“ Commission ” means the Securities and Exchange Commission.

“ Common Stock ” has the meaning set forth in the preamble hereto.

2

“ Company ” has the meaning set forth in the preamble hereto.

“ Debentures ” has the meaning set forth in the preamble hereto.

“ Effectiveness Period ” has the meaning set forth in Section 2(a)(iii) hereof.

“ Effectiveness Target Date ” has the meaning set forth in Section 2(a)(ii) hereof.

“ Exchange Act ” means the Securities Exchange Act of 1934, as amended.

“ Holder ” means a Person who owns, beneficially or otherwise, Transfer Restricted Securities.

“ Indemnified Holder ” has the meaning set forth in Section 6(a) hereof.

“ Indenture ” means the Indenture, dated as of July 6, 2004 between the Company and LaSalle Bank, N.A., as trustee, pursuant to which the Debentures are to be issued, as such Indenture is amended, modified or supplemented from time to time in accordance with the terms thereof.

“ Initial Purchasers ” has the meaning set forth in the preamble hereto.

“ Liquidated Damages ” has the meaning set forth in Section 3(b) hereof.

“ Liquidated Damages Payment Date ” means each July 15 ^th and January 15 ^th .

“ Majority of Holders ” means Holders holding over 50% of the aggregate principal amount of Debentures outstanding; provided that, for the purpose of this definition, a Holder of shares of Common Stock that constitute Transfer Restricted Securities shall be deemed to hold an aggregate principal amount of Debentures (in addition to the principal amount of Debentures held by such Holder) equal to the product of (A) the quotient of (x) the number of such shares of Common Stock held by such Holder and (y) the conversion rate (as expressed in the number of shares of Common Stock issuable per $1,000 principal amount of Debentures) in effect at the time of the conversion of Debentures into such shares of Common Stock as determined in accordance with the Indenture and (B) $1,000.

“ NASD ” means the National Association of Securities Dealers, Inc.

“ Notice and Questionnaire ” means a written notice executed by a Holder and delivered to the Company containing substantially the information called for by the Selling Securityholder Notice and Questionnaire attached as Annex A to the Offering Memorandum of the Company dated June 29, 2004 relating to the Debentures.

3

“ Notice Holder ” means on any date, any Holder that has delivered a Notice and Questionnaire to the Company on or prior to such date.

“ Person ” means an individual, partnership, corporation, limited liability company, association, joint-stock company, unincorporated organization, trust, joint venture or a government or agency or political subdivision thereof.

“ Purchase Agreement ” has the meaning set forth in the preamble hereto.

“ Prospectus ” means the prospectus included in a Shelf Registration Statement, as amended or supplemented by all prospectus supplements and by all amendments thereto, including post-effective amendments, and all material incorporated by reference into such prospectus.

“ Record Holder ” means with respect to any Liquidated Damages Payment Date, each Person who is a Holder on the 15 ^th day preceding the relevant Liquidated Damages Payment Date, including a Holder that owns shares of Common Stock which constitute Transfer Restricted Securities on the 15 ^th day preceding the relevant Liquidated Damages Payment Date.

“ Registration Default ” has the meaning set forth in Section 3(a) hereof.

“ Securities Act ” means the Securities Act of 1933, as amended.

“ Shelf Filing Deadline ” has the meaning set forth in Section 2(a)(i) hereof.

“ Shelf Registration Statement ” has the meaning set forth in Section 2(a)(i) hereof.

“ Subsequent Shelf Registration Statement ” has the meaning set forth in Section 2(c) hereof.

“ Suspension Notice ” has the meaning set forth in Section 4(c) hereof.

“ Suspension Period ” has the meaning set forth in Section 4(b)(i) hereof.

“ TIA ” means the Trust Indenture Act of 1939, as amended, and the rules and regulations of the Commission thereunder, in each case, as in effect on the date the Indenture is qualified under the TIA.

“ Transfer Restricted Securities ” means each Debenture and each share of Common Stock issued upon conversion of any Debenture until the earliest of:

(i) the date on which such Debenture or such share of Common Stock issued upon conversion has been effectively registered under the Securities Act and disposed of in accordance with the Shelf Registration Statement;

4

(ii) the date on which such Debenture or such share of Common Stock issued upon conversion is transferred in compliance with Rule 144 under the Securities Act (or any similar provision then in effect) or may be sold or transferred by a Person who is not an affiliate of the Company pursuant to Rule 144(k) under the Securities Act (or any other similar provision then in effect); or

(iii) the date on which such Debenture or such share of Common Stock issued upon conversion ceases to be outstanding (whether as a result of redemption, repurchase and cancellation, conversion or otherwise).

“ Trustee ” means LaSalle Bank, N.A., the trustee under the Indenture, and its permitted successors and assigns.

“ Underwritten Registration ” means a registration in which Debentures of the Company are sold to an underwriter for reoffering to the public.

Unless the context otherwise requires, the definitions set forth in this Section 1 shall be equally applicable to both the singular and plural forms.

2. Shelf Registration .

(a) The Company shall:

(i) not later than 120 days after the date hereof (the “ Shelf Filing Deadline ”), cause to be filed a registration statement pursuant to Rule 415 under the Securities Act (the “ Shelf Registration Statement ”), which Shelf Registration Statement shall provide for resales of all Transfer Restricted Securities held by Holders that have provided the information required pursuant to the terms of Section 2(b) hereof;

(ii) use its commercially reasonable efforts to cause the Shelf Registration Statement to be declared effective by the Commission not later than 210 days after the date hereof (the “ Effectiveness Target Date ”); and

(iii) use its commercially reasonable efforts to keep the Shelf Registration Statement continuously effective, supplemented and amended as required by the provisions of Section 4(b) hereof to the extent necessary to ensure that (A) it is available for resales by the Holders entitled to the benefit of this Agreement and (B) it conforms with the requirements of this Agreement and the Securities Act and the rules and regulations of the Commission promulgated thereunder as announced from time to time, for a period (the “ Effectiveness Period ”) until the earliest of:

(1) the second anniversary of the last date of original issuance of any of the Debentures;

5

(2) the date on which Holders that are not affiliates of the Company (as defined in Rule 144 under the Securities Act) are able to sell all Transfer Restricted Securities immediately without restriction pursuant to the volume limitation provisions of Rule 144 under the Securities Act; or

(3) the date on which all of the Transfer Restricted Securities are sold pursuant to the Shelf Registration Statement or pursuant to Rule 144 under the Securities Act or any similar provision then in effect.

(b) At the time the Shelf Registration Statement is declared effective, each Holder that became a Notice Holder on or prior to the date five (5) Business Days prior to such time of effectiveness shall be named as a selling securityholder in the Shelf Registration Statement and the related Prospectus in such a manner as to permit such Holder to deliver such Prospectus to purchasers of Transfer Restricted Securities in accordance with applicable law. None of the Company’s securityholders (other than Holders that have complied with the provisions of this Agreement) shall have the right to include any of the Company’s securities in the Shelf Registration Statement.

(c) If the Shelf Registration Statement or any Subsequent Shelf Registration Statement ceases to be effective for any reason at any time during the Effectiveness Period (other than because all Transfer Restricted Securities registered thereunder shall have been resold pursuant thereto or shall have otherwise ceased to be Transfer Restricted Securities), the Company shall use its commercially reasonable efforts to obtain the prompt withdrawal of any order suspending the effectiveness thereof, and in any event shall within thirty (30) days of such cessation of effectiveness amend the Shelf Registration Statement in a manner reasonably expected to obtain the withdrawal of the order suspending the effectiveness thereof, or file an additional Shelf Registration Statement covering all of the securities that as of the date of such filing are Transfer Restricted Securities ( a “ Subsequent Shelf Registration Statement ”). If a Subsequent Shelf Registration Statement is filed, the Company shall use its commercially reasonable efforts to cause the Subsequent Shelf Registration Statement to become effective as promptly as is practicable after such filing and to keep such Subsequent Shelf Registration Statement continuously effective until the end of the Effectiveness Period.

6

(d) The Company shall supplement and amend the Shelf Registration Statement if required by the rules, regulations or instructions applicable to the registration form used by the Company for such Shelf Registration Statement, if required by the Securities Act or as reasonably requested in writing by the Initial Purchasers or by the Trustee on behalf of the Holders covered by such Shelf Registration Statement.

(e) Each Holder agrees that if such Holder wishes to sell Transfer Restricted Securities pursuant to the Shelf Registration Statement and related Prospectus, it will do so only in accordance with this Section 2(e) and Section 4. From and after the date the Shelf Registration Statement is declared effective the Company shall, as promptly as practicable after the date a Notice and Questionnaire is received by the Company, and in any event upon the later of (x) thirty (30) Business Days after such date or (y) thirty (30) Business Days after the expiration of any Suspension Period in effect when the Notice and Questionnaire is delivered or put into effect within thirty (30) Business Days of such delivery date:

(i) if required by applicable law, file with the SEC a post-effective amendment to the Shelf Registration Statement or prepare and, if required by applicable law, file a supplement to the related Prospectus or a supplement or amendment to any document incorporated therein by reference or file any other required document so that the Holder delivering such Notice and Questionnaire is named as a selling securityholder in the Shelf Registration Statement and the related Prospectus in such a manner as to permit such Holder to deliver such Prospectus to purchasers of the Transfer Restricted Securities in accordance with applicable law and, if the Company shall file a post-effective amendment to the Shelf Registration Statement, use its commercially reasonable efforts to cause such post-effective amendment to be declared effective under the Securities Act as promptly as is practicable, but in any event by the date (the “Amendment Effectiveness Deadline Date” ) that is forty-five (45) days after the date such post effective amendment is required by this clause to be filed;

(ii) upon its request, provide such Holder copies of any documents filed pursuant to Section 2(e)(i) hereof; and

(iii) notify such Holder as promptly as practicable after the effectiveness under the Securities Act of any post-effective amendment filed pursuant to Section 2(e)(i) hereof;

provided that if such Notice and Questionnaire is delivered during a Suspension Period or a Suspension Period begins within thirty (30) Business Days after the delivery of such Notice and Questionnaire, the Company shall so inform the Holder delivering such Notice and Questionnaire and shall take the actions set

7

forth in clauses (i), (ii) and (iii) above within thirty (30) Business Days after the expiration of the Suspension Period in accordance with Section 4(b); and provided , further , that the Company shall not be required to file more than one amendment to the Shelf Registration Statement or supplement to the Prospectus pursuant to this Section 2(e) to name additional Holders in any two calendar month period, and to the extent a completed Notice and Questionnaire is received by the Company from a Holder in any two-month period in which the Company has already filed such an amendment or supplement, the Company shall not be required to file an amendment or supplement to name additional Holders in respect of such Holder until the later of (x) the first Business Day in the following two-month period and (y) within ten (10) Business Days after receipt of the Holder’s completed Notice and Questionnaire. Notwithstanding anything contained herein to the contrary, (i) the Company shall be under no obligation to name any Holder that is not a Notice Holder as a selling securityholder in any Registration Statement or related Prospectus and (ii) the Amendment Effectiveness Deadline Date shall be extended by up to ten (10) Business Days from the expiration of a Suspension Period (and the Company shall incur no obligation to pay Liquidated Damages during such extension) if such Suspension Period shall be in effect on the Amendment Effectiveness Deadline Date.

3. Liquidated Damages.

(a) Each event referred to in the following clauses (i) through (iv) is a “ Registration Default ”:

(i) the Shelf Registration Statement is not filed with the Commission prior to or on the Shelf Filing Deadline;

(ii) the Shelf Registration Statement has not been declared effective by the Commission prior to or on the Effectiveness Target Date;

(iii) except as provided in Section 4(b)(i) hereof, the Shelf Registration Statement is filed and declared effective but, during the Effectiveness Period, shall thereafter cease to be effective or fail to be usable for its intended purpose without being succeeded within ten (10) Business Days (or, if any Suspension Period is then in effect, the fifth Business Day following the expiration of such Suspension Period) by a post-effective amendment to the Shelf Registration Statement, a supplement to the Prospectus or a report filed with the Commission pursuant to Section 13(a), 13(c), 14 or 15(d) of the Exchange Act that cures such failure and, in the case of a post-effective amendment, is itself immediately declared effective; or

(iv) (A) prior to or on the 45th or 60th day, as the case may be, of any Suspension Period, such suspension has not been terminated or (B) the Suspension Periods exceed an aggregate of 120 days in any 360-day period.

8

For purposes of this Agreement, each Registration Default set forth above shall begin and be cured on the dates set forth in the table below:

(b) If a Registration Default occurs

(A) in respect of the Debentures, to each Holder of Debentures, other than a Registration Default relating to a failure to file or have an effective Shelf Registration Statement with respect to shares of Common Stock issuable upon conversion of the Debentures that are Transfer Restricted Securities, the Company hereby agrees to pay interest (“ Liquidated Damages ”) with respect to the Debentures that are Transfer Restricted Securities from and

9

including the day following the beginning of the Registration Default to but excluding the earlier of (1) the day on which the Registration Default has been cured and (2) the date the Shelf Registration Statement is no longer required to be kept effective, accruing at a rate (x) with respect to the first 90-day period during which a Registration Default shall have occurred and be continuing, equal to 0.25% per annum of the aggregate principal amount of the Debentures that are Transfer Restricted Securities, and (y) with respect to the period commencing on the 91st day following the day the Registration Default shall have occurred and be continuing, equal to 0.50% per annum of the aggregate principal amount of the Debentures that are Transfer Restricted Securities; provided that in no event shall Liquidated Damages accrue at a rate per year exceeding 0.50% of the aggregate principal amount of the Debentures that are Transfer Restricted Securities; and

(B) in respect of any shares of Common Stock, to each Holder of shares of Common Stock issued upon conversion of the Debentures, no Liquidated Damages on such Common Stock will be payable, but the Holder of such shares of Common Stock shall be entitled to receive additional Common Stock upon conversion (except to the extent that the Company elects to deliver cash upon conversion).

Notwithstanding the provisions in this Section 3(b), if any Liquidated Damages are payable as a result of the Company’s failure to add the name of a Holder as a selling securityholder in the Shelf Registration Statement and the related Prospectus in such a manner as to permit such Holder to deliver such Prospectus to purchasers of the Transfer Restricted Securities and if such failure shall have not resulted in a Registration Default with respect to the other Holders, only such Holder that was not named as a selling securityholder shall be entitled to receive such Liquidated Damages.

(c) All accrued Liquidated Damages shall be paid in arrears to Record Holders by the Company on each Liquidated Damages Payment Date. Upon the cure of all Registration Defaults relating to any particular Debenture or share of Common Stock, the accrual of Liquidated Damages with respect to such Debenture or share of Common Stock will cease.

(d) All obligations of the Company set forth in this Section 3 that are outstanding with respect to any Transfer Restricted Security at the time such security ceases to be a Transfer Restricted Security shall survive until such time as all such obligations with respect to such Transfer Restricted Security shall have been satisfied in full.

10

The parties hereto agree that the Liquidated Damages provided for in this Section 3 constitute a reasonable estimate of the damages that may be incurred by Holders by reason of any Registration Default. The Liquidated Damages set forth above shall be the exclusive monetary remedy available to the Holders for each Registration Default.

4. Registration Procedures.

(a) In connection with the Shelf Registration Statement, the Company shall comply with all the provisions of Section 4(b) hereof and shall use its commercially reasonable efforts to effect such registration to permit the sale of the Transfer Restricted Securities, and pursuant thereto, shall as promptly as is practicable but no later than the Shelf Filing Deadline prepare and file with the Commission a Shelf Registration Statement relating to the registration on any appropriate form under the Securities Act.

(b) In connection with the Shelf Registration Statement and any Prospectus required by this Agreement to permit the sale or resale of Transfer Restricted Securities, the Company shall:

(i) Subject to any notice by the Company in accordance with Section 4(b) hereof of the existence of any fact or event of the kind described in Section 4(b)(iii)(D) hereof, use its commercially reasonable efforts to keep the Shelf Registration Statement continuously effective during the Effectiveness Period; upon the occurrence of any event that would cause the Shelf Registration Statement, any amendment thereto, any document incorporated by reference therein or the Prospectus contained therein (A) to contain a material misstatement or omission or (B) not to be effective and usable for resale of Transfer Restricted Securities during the Effectiveness Period, the Company shall file as promptly as is practicable an appropriate amendment to the Shelf Registration Statement, a supplement to the Prospectus or a report filed with the Commission pursuant to Section 13(a), 13(c), 14 or 15(d) of the Exchange Act, in the case of clause (A), correcting any such misstatement or omission, and, in the case of either clause (A) or (B), use its commercially reasonable efforts to cause such amendment to be declared effective and the Shelf Registration Statement and the related Prospectus to become usable for their intended purposes as soon as practicable thereafter. Notwithstanding the foregoing, the Company may suspend the effectiveness of the Shelf Registration Statement by written notice

11

to the Holders for a period not to exceed an aggregate of 45 days in any 90-day period (each such period, a “ Suspension Period ”) if:

(x) an event occurs and is continuing as a result of whic