Territorial Health Parity Act of 2009

Territorial Health Parity Act of 2009 - Amends title XI of the Social Security Act (SSA) to sunset at the end of FY2009 the limitation on Medicaid payments to Puerto Rico, the Virgin Islands, Guam, the Northern Mariana Islands, and American Samoa.

Amends SSA title XIX (Medicaid) to: (1) repeal, as of the end of FY2011, the federal medical assistance percentage (FMAP) of 50% that applies to such territories; and (2) set the new FMAP for such territories at one determined by the Secretary of Health and Human Services (Secretary) in consultation with the Secretary of the Interior. Specifies a transitional FMAP for such territories for FY2010-FY2011.

Requires the Secretary to report to Congress on the per capita income data used to promulgate the FMAP in the territories and how such data differ from the per capita income data used to promulgate FMAPs for the 50 states and the District of Columbia. Requires the report to include recommendations on how FMAPs can be calculated for the territories to ensure parity with the 50 states and the District of Columbia.

Amends the Personal Responsibility and Work Opportunity Reconciliation Act of 1996 to extend the Medicaid program to the citizens of the Freely Associated States (Federated States of Micronesia, the Republic of the Marshall Islands, and the Republic of Palau).

Amends SSA title XIX to set a 100% FMAP for otherwise qualified services rendered to such citizens.