The human autoimmune regulator gene (AIRE), responsible for autoimmune polyglandular syndrome Type 1 (APS1), has recently been identified by positional cloning. Here we report the cloning of Aire, the mouse homologue of AIRE, and the characterization of its genomic structure. The complete Aire gene is contained in 14 exons and encodes a protein of 552 amino acids. The coding region shares 77% nucleotide homology and 71% protein homology with human AIRE. As in its human homologue, Aire contains two PHD-type zinc-finger motifs, suggesting that the Aire protein may act as a transcription regulator.