340B Program Improvement and Integrity Act of 2009

340B Program Improvement and Integrity Act of 2009 - Amends the Public Health Service Act to expand the drug discount program to allow participation as a covered entity by certain: (1) children's hospitals; (2) critical access hospitals; (3) entities providing maternal and child health services, community mental health services, or treatment services for substance abuse; (4) Medicare-dependent, small rural hospitals; (5) sole community hospitals; and (6) rural referral centers. Prohibits enrolled hospitals from obtaining covered outpatient drugs through a group purchasing arrangement. Requires the Secretary of Health and Human Services to establish reasonable exceptions to such requirements, including for drugs unavailable through the program and to facilitate generic substitution when a generic covered drug is available at a lower price.

Expands the program to include a drug used in connection with an inpatient or outpatient service by enrolled hospitals. (Currently, only outpatient drugs are covered under the program.)

Requires hospitals enrolled in the 340B drug discount program to provide to each state a credit on the estimated annual costs to such hospital of single source and innovator multiple source drugs and noninnovator multiple source drugs provided to Medicaid recipients for inpatient use. Sets forth a formula for calculating the credit. Allows a hospital to avoid paying such credits under certain circumstances.

Requires the Secretary to: (1) carry out activities to improve compliance by manufacturers and covered entities with the requirements of the drug discount program; and (2) establish an administrative process for resolving claims by covered entities and manufacturers of violations of such requirements.

Requires manufacturers to offer each covered entity covered drugs for purchase at or below the applicable ceiling price if such a drug is made available to any other purchaser at any price.