JAZZ PHARMACEUTICALS, INC. WAIVER AND AMENDMENT AGREEMENT

Exhibit 4. 3B

JAZZ PHARMACEUTICALS, INC.

WAIVER AND AMENDMENT AGREEMENT

THIS WAIVER AND AMENDMENT AGREEMENT (the “Agreement”) is made effective as of March 12, 2008 (the “Effective Date”), by and among JAZZ PHARMACEUTICALS, INC., a Delaware corporation (the “Company”), and the undersigned Holders (the “Consenting Holders”).

RECITALS

WHEREAS, the Company and the Investors are parties to that certain Third Amended and Restated Investor Rights Agreement made effective as of June 6, 2007 (the “Investor Rights Agreement”).

WHEREAS, the Consenting Holders acknowledge that the Company expects to enter into a Registration Rights Agreement in substantially the form attached hereto as Exhibit A (the “Registration Rights Agreement”) with certain purchasers (the “Purchasers”) of senior secured notes and warrants to purchase shares of the Company’s Common Stock (the “Warrant Shares”) pursuant to the terms of a Senior Secured Note and Warrant Purchase Agreement by and among the Company, JPI Commercial, LLC and the Purchasers (the “Note and Warrant Purchase Agreement”).

WHEREAS, the Consenting Holders acknowledge that pursuant to the terms of the Registration Rights Agreement, the Company will be obligated to prepare and file a registration statement (the “Resale Registration Statement”) under the Securities Act of 1933, as amended (the “Securities Act”), registering the resale of the Warrant Shares from time to time by the Purchasers (or any subsequent transferees or assignees thereof). As used in this Agreement, (i) the term “Warrant Shares” also includes any shares of the Company’s Common Stock issued as (or issuable upon the conversion or exercise of any warrant, right or other security that is issued as) a dividend or other distribution with respect to, or in exchange for, or in replacement of, the Warrant Shares; and (ii) the term “Resale Registration Statement” also includes (A) any registration statement filed by the Company under the Securities Act pursuant to the terms of the Registration Rights Agreement and (B) any amendments or supplements to any of such registration statements.

WHEREAS, pursuant to Section 4 of the Investor Rights Agreement, the Holders have under certain circumstances the right to be notified if the Company decides to Register any of its Common Stock and to include certain Registrable Securities held by such Holders in such Registration (and any related qualification under Blue Sky laws or other compliance), and in any underwriting involved therein (the “Piggyback Registration Rights”).

WHEREAS, pursuant to Section 15.5 of the Investor Rights Agreement, the Company and the Consenting Holders (for and on behalf of all Holders and all Investors) wish to (i) amend the Investor Rights Agreement as set forth below; and (ii) waive each of (A) the Piggyback Registration Rights in connection with the filing of the Resale Registration Statement and any offerings made pursuant thereto and (B) the provisions of Section 10 of the Investor Rights Agreement with respect to the entering into of the Registration Rights Agreement by the Company and the grant to the Purchasers of Registration rights pursuant thereto.

WHEREAS, the Consenting Holders are holders of at least 60% of the Registrable Securities held by all Holders and, together with the Company, have the right, pursuant to Section 15.5 of the Investor Rights Agreement, to amend the Investor Rights Agreement and to waive certain provisions thereof.

1

NOW, THEREFORE, in consideration of the mutual agreements, covenants and considerations contained herein, the Company and the Consenting Holders agree as follows:

AGREEMENT

1.1 The Consenting Holders hereby waive, for and on behalf of all Holders and all Investors, the provisions of Section 10 of the Investor Rights Agreement with respect to the entering into of the Registration Rights Agreement by the Company and the grant to the Purchasers of Registration rights pursuant thereto. In furtherance of the foregoing, the Consenting Holders hereby provide, for and on behalf of all Holders and all Investors, express written consent to the entering into by the Company of the Registration Rights Agreement and to the consummation by the Company of the transactions contemplated thereby, including but not limited to the grant of Registration rights to the Purchasers and the filing of the Resale Registration Statement pursuant thereto.

1.2 The Consenting Holders hereby further waive, for and on behalf of all Holders and all Investors, (i) any and all Piggyback Registration Rights in connection with the filing of, and any offerings made pursuant to, the Resale Registration Statement and (ii) any rights to any notices with respect to the foregoing under the Investor Rights Agreement.

1.3 The foregoing waivers in Sections 1.1 and 1.2 are irrevocable and shall be effective with respect to each Holder and each Investor, as well as all affiliates, successors, heirs, executors, administrators and assigns of each such Holder and Investor.

2.1 Section 1.1. Section 1.1 of the Investor Rights Agreement is hereby amended and restated to read in full as follows:

“1.1 “Affiliate” shall mean, with respect to any Person, a Person directly or indirectly controlling, controlled by, or under common control with, such Person; provided, however, that, except for purposes of Section 11.2, no Series BB Holder shall be considered an Affiliate of any other Person except to the extent, and only to the extent, that such Series BB Holder holds shares of Common Stock issued upon conversion of the Convertible Securities other than shares of Common Stock issued upon exercise of the Series BB Warrants.”

2.2 Section 1.19. Section 1.19 of the Investor Rights Agreement is hereby amended and restated to read in full as follows:

“1.19 “Registrable Securities” shall mean (i) any Common Stock now owned or hereafter acquired by a Manager, (ii) any Common Stock issued upon conversion of the Convertible Securities, (iii) any Common Stock issued upon exercise of the Series BB Warrants, and (iv) any Common Stock issued (or issuable upon conversion or exercise of any warrant, right or other security which is issued) upon stock dividends, subdivisions, stock splits, recapitalization, merger or other distributions with respect to, or in exchange for, or in replacement of, such securities identified in clauses (i), (ii) and (iii) and this clause (iv), provided, however, that no shares of Common Stock shall be deemed Registrable Securities for purposes of this Agreement to the extent that such shares of Common Stock (A) have been sold to the public through a Registration Statement or

2

pursuant to Rule 144; (B) have been sold, transferred or otherwise disposed by a person in a transaction in which its rights under this Agreement were not assigned; or (C) are held by a Holder or Investors whose rights to cause the Company to register securities pursuant to this Agreement have terminated in accordance with Section 6 of this Agreement.”

2.3 Section 1.23. Section 1.23 of the Investor Rights Agreement is hereby amended and restated to read in full as follows:

“1.23 “Series BB Holder” means a holder of (i) warrants originally exercisable for shares of the Company’s Series BB Preferred Stock, which such warrants (A) were originally issued pursuant to a Senior Secured Note and Warrant Purchase Agreement, dated June 24, 2005, by and among the Company and certain of the Investors and (B) automatically became exercisable for shares of Common Stock in connection with the Initial Public Offering (the “Series BB Warrants”); or (ii) shares of Common Stock issued upon exercise of the Series BB Warrants.”

2.4 Section 1.24. Section 1.24 of the Investor Rights Agreement is hereby amended and restated to read in full as follows:

“1.24 “Special Registration Statement” shall mean (i) any registration statement relating to any employee benefit plan; (ii) with respect to any corporate reorganization or transaction under Rule 145 of the Securities Act, any registration statement related to the issuance or resale of securities issued in such a transaction; (iii) any registration statement related to stock issued upon conversion of debt securities; (iv) any Registration effected pursuant to the terms of the Registration Rights Agreement; or (v) any WKSI Shelf Registration Statement that the Company’s Board of Directors shall, in its sole discretion, designate as a “Special Registration Statement” for purposes of this Agreement.”

2.5 Section 1.26. Section 1.26 is hereby added to the Investor Rights Agreement and shall read in full as follows:

“1.26 “Purchase Agreement” means that certain Stock Purchase Agreement, dated as of January 27, 2004, by and among the Company and certain of the Investors, as amended from time to time in accordance with the terms thereof.”

2.6 Section 1.27. Section 1.27 is hereby added to the Investor Rights Agreement and shall read in full as follows:

“1.27 “Registration Rights Agreement” means that certain Registration Rights Agreement, dated as of March 17, 2008, by and among the Company and the purchasers listed on Schedule A thereto, as the same may be amended from time to time in accordance with the terms thereof.”

2.7 Section 12. Section 12 of the Investor Rights Agreement is hereby amended and restated to read in full as follows:

“12. Market Standoff. Each Holder hereby agrees that, if so requested by the Company and the Underwriter’s Representative (if any), such Holder shall not sell, make any short sale of, loan, grant any option for the purchase of, or otherwise transfer or dispose of any Registrable Securities or other securities (except for the Warrant Shares and the warrants

3

issued pursuant to the Note and Warrant Purchase Agreement) of the Company (“Market Standoff”) without the prior written consent of the Company and the Underwriter’s Representative for such period of time commencing with the date the Company provides notice to the Holders of a proposed follow-on offering pursuant to Section 4.1 or otherwise (including Registrations initiated pursuant to Section 3) and ending 90 days after the effective date of the Registration Statement with respect to the follow-on offering or, in the event of a shelf registration, the date of the prospectus supplement for such follow-on offering, as may be requested by the Underwriter’s Representative; provided, however, that a Holder shall not be required to agree to a Market Standoff for a period of time that commences less than 30 days after the expiration of another period of time during which the Holder has agreed to a Market Standoff. The obligations of the Holders under this Section 12 shall be conditioned upon similar agreements being in effect with each other stockholder who is an officer or director. In order to enforce the covenants set forth in this Section 12, the Company may impose stop-transfer instructions with respect to the securities of the Holder (and the securities of every other Person subject to the restrictions in this Section 12).”

3.1 Defined Terms. Capitalized terms not otherwise defined herein shall have the meanings ascribed to them in the Investor Rights Agreement.

3.2 Full Power and Authority. Each Consenting Holder represents and warrants to the Company that (i) such Consenting Holder has the full right, power and authority to execute and deliver this Agreement, and (ii) this Agreement has been duly executed and delivered by such Consenting Holder and constitutes the legal, valid and binding obligation of such Consenting Holder enforceable in accordance with its terms, except (A) as such enforcement is limited by bankruptcy, insolvency or other similar laws affecting the enforcement of creditors’ rights generally and (B) for limitations imposed by general principles of equity.

3.3 Effect of Agreement. Except as modified by the terms of this Agreement, the terms and provisions of the Investor Rights Agreement shall remain in full force and effect. Other than as stated in this Agreement, this Agreement shall not operate as a waiver of any condition or obligation imposed on the parties under the Investor Rights Agreement. In the event of any conflict, inconsistency, or incongruity between any provision of this Agreement and any provision of the Investor Rights Agreement, the provisions of this Agreement shall govern and control. This Agreement shall not be changed or modified orally, but only by an instrument in writing signed by the parties hereto.

3.4 Governing Law. This Agreement shall be governed by, and construed in accordance with, the laws of the State of California excluding those laws that direct the application of the laws of another jurisdiction.

3.5 Successors and Assigns. The provisions hereof shall inure to the benefit of, and be binding upon, the successors, assigns, heirs, executors and administrators of the parties hereto and each Holder and Investor, and shall be enforceable by the Company or any Holder or Investor.

3.6 Counterparts. This Agreement may be executed in several counterparts, each of which shall constitute an original and all of which, when taken together, shall constitute one instrument.

4

3.7 Certain Confidential Information. Certain of the information contained in this Agreement is confidential and has not been publicly disclosed by the Company, including the transactions contemplated by the Note and Warrant Purchase Agreement and the contemplated filing of the Resale Registration Statement pursuant to the terms of the Registration Rights Agreement (the “Confidential Information”). Accordingly, each of the undersigned Holders agrees to maintain the Confidential Information in confidence until such time as the Confidential Information has been publicly disclosed by the Company.

[REMAINDER OF PAGE INTENTIONALLY LEFT BLANK]

5

IN WITNESS WHEREOF, the undersigned have executed this AGREEMENT effective as of the Effective Date.

SIGNATURE PAGE TO

WAIVER AND AMENDMENT AGREEMENT

IN WITNESS WHEREOF, the undersigned have executed this AGREEMENT effective as of the Effective Date.

INVESTORS:

SIGNATURE PAGE TO

WAIVER AND AMENDMENT AGREEMENT

IN WITNESS WHEREOF, the undersigned have executed this AGREEMENT effective as of the Effective Date.

INVESTORS:

SIGNATURE PAGE TO

WAIVER AND AMENDMENT AGREEMENT

IN WITNESS WHEREOF, the undersigned have executed this AGREEMENT effective as of the Effective Date.

INVESTORS:

SIGNATURE PAGE TO

WAIVER AND AMENDMENT AGREEMENT

IN WITNESS WHEREOF, the undersigned have executed this AGREEMENT effective as of the Effective Date.

INVESTORS:

SIGNATURE PAGE TO

WAIVER AND AMENDMENT AGREEMENT

IN WITNESS WHEREOF, the undersigned have executed this AGREEMENT effective as of the Effective Date.

INVESTORS:

SIGNATURE PAGE TO

WAIVER AND AMENDMENT AGREEMENT

IN WITNESS WHEREOF, the undersigned have executed this AGREEMENT effective as of the Effective Date.

INVESTORS:

SIGNATURE PAGE TO

WAIVER AND AMENDMENT AGREEMENT