Mutations in the autoimmune regulator (AIRE) protein are the causative factor in development of the human disease autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy (APECED). In mice, the absence of the analogous protein aire influences ectopic expression of peripheral tissue antigens in thymic medullary epithelial cells (MECs), resulting in the development of an autoimmune disorder similar to APECED and establishing aire/AIRE as an important player in the induction of central tolerance. However, the molecular mechanism of AIRE's function, in particular its ability to specifically control the expression of peripheral tissue antigens in MECs, is still unclear. Here, we review current evidence relating to the molecular mechanism of AIRE.