Medicare Care Transitions Program Act of 2009 - Amends title XVIII (Medicare) of the Social Security Act to direct the Secretary of Health and Human Services to establish a Care Transitions Program under which outcomes-based payments are made to community-based transitional care (CTC) suppliers for: (1) furnishing care transition services to an individual after discharge from inpatient care; (2) improving quality of care; and (3) reducing rehospitalization rates.