Harvey Milk, the first openly gay elected politician in the United States, and former Republican congressman and vice presidential candidate Jack Kemp were honoured posthumously.
Other recipients include US health-care advocates, an American-Indian tribal chief and the Hispanic actress Chita Rivera. Long-time US civil rights leader Reverend Joseph Lowery was honoured.
Nancy Goodman Brinker, whose organization is the largest breast cancer awareness group, as well as Doctor Pedro Jose Greer and American Indian chief Joe Medicine Crow-High Bird, were given medals.
Doctor Janet Davison Rowley, whose breakthrough in determining a key cause of leukemia and other cancers was among the most important medical breakthroughs of the past century, also received a Medal of Freedom.
Kennedy, whose sister Eunice Kennedy Shriver died on Tuesday, did not attend the ceremony.