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Autoimmune polyendocrinopathies are traditionally divided into two distinct syndromes, autoimmune polyendocrine syndrome type 1 and 2 (APS-1 and -2). The first is a monogenic disease caused by mutations in the autoimmune regulator (AIRE) gene, the second is associated with variants in immune genes, in particular certain major histocompatibility complex genotypes, but also to coding variants in AIRE. Even if each syndrome have distinct features, there is also considerably overlap in phenotypes and circulating autoantibodies. In this overview recent progress in the understanding of pathogenic mechanisms and clinical features of APS-1 and -2 is summarized highlighting the role of AIRE in both conditions.