Autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy (APECED) is a rare autosomal recessive disorder defined by the presence of two of three conditions, namely, Addison's disease, hypoparathyroidism, and mucocutaneous candidiasis. APECED is caused by alteration in a single gene, named the autoimmune regulator (AIRE) gene. We report AIRE gene mutations in a Japanese female with APECED. The patient is a 22-year-old Japanese female who was diagnosed with Addison's disease, hypoparathyroidism, and mucocutaneous candidiasis at age 8 years. Sequence analysis of the AIRE gene revealed novel compound heterozygous mutations. One was 1471 delCinsTT in exon 11 (GenBank accession no. AB006682), which leads to a frameshift and premature truncation of a 502 amino acid protein. The other was a G-->A transition at IVS11+1. Her mother was heterozygous for 1471 delCinsTT and was normal homozygous for IVS11+1. We found novel compound heterozygous mutations in the AIRE gene of a Japanese female with APECED.