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; and (3) rural referral centers. Expands the program to include drugs used in connection with an inpatient or outpatient service by enrolled hospitals (currently, only outpatient drugs are covered under the program).

Prohibits enrolled hospitals from obtaining covered outpatient drugs through a group purchasing arrangement. Requires the Secretary of Health and Human Services (HHS) to establish reasonable exceptions to such prohibition, including for drugs unavailable through the program and to facilitate generic substitution when a generic covered drug is available at a lower price.

Requires a hospital enrolled in the 340B drug discount program to issue a credit to a state Medicaid program for inpatient drugs provided to Medicaid recipients.

Requires the Secretary to: (1) provide for improvements in compliance by manufacturers and covered entities with the requirements of the drug discount program; and (2) establish and implement 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.