The maintenance of immunologic self-tolerance requires the coordination of multiple complementary systems. Studies of the Autoimmune Regulator (Aire) gene have revealed that Aire promotes self-tolerance in part by inducing the transcription of a wide array of tissue-specific antigens (TSAs), particularly in the thymus. The importance of Aire is highlighted by the fact that patients and mice defective in Aire expression develop a multi-organ autoimmune syndrome. In this review we discuss recent progress in our understanding of Aire’s control of immune tolerance at the cellular and molecular levels, and also address the potential importance of Aire expression both in the thymus and in the peripheral lymphoid organs. The detection of both Aire and TSA expression by cell populations outside of the thymus raises the possibility that such expression may play a relevant role in the maintenance of self-tolerance.