Tribal Health Benefits Clarification Act of 2009 - Amends the Internal Revenue Code to allow an exclusion from gross income for certain medical care or benefits provided to American Indians, including: (1) certain health services or benefits provided or purchased by the Indian Health Service; (2) specified medical care provided by an Indian tribe or tribal organization to a member of an Indian tribe; (3) the value of accident or health plan coverage provided by an Indian tribe or tribal organization for medical care to a member of an Indian tribe; and (4) any other medical care provided by an Indian tribe that supplements, replaces, or substitutes for federal programs and services provided to Indian tribes or Indians.