Abstract Objective Autoimmune polyendocrinopathy–candidiasis–ectodermal dystrophy (APECED) causes multiple endocrine deficiencies, oral candidiasis and different forms of ectodermal dystrophy including enamel hypoplasia, documented in permanent teeth. Our purpose was to examine dental aberrations associated with APECED, including possible manifestations in primary teeth. Design We studied clinically, radiographically, and by scanning electron microscopy (SEM) teeth of children belonging to two APECED families with different mutations in the AIRE gene. Results In addition to enamel defects in the permanent teeth we observed hypoplastic pits and hypomaturated patches in the deciduous teeth with underlying changes in the prismatic ultrastructure. The enamel of the permanent molars exhibited a layered arrangement with included whirl-like formations. Conclusions Our findings confirm that APECED causes enamel defects that are individually but chronologically distributed, and can alter enamel development early enough to affect deciduous teeth.