Autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy (APECED) (or autoimmune polyendocrine syndrome type 1) is a rare autosomal recessive disorder caused by mutations in the autoimmune regulator gene. It causes a loss in central immune tolerance, failure to eliminate autoreactive T cells in the thymus, and their escape to the periphery. APECED patients are susceptible to mucocutaneous candidiasis and multiple endocrine and nonendocrine autoimmune diseases. Although it depends on the series, approximately 25% of APECED patients are affected by gastrointestinal (GI) manifestations, mainly autoimmune-related disorders like autoimmune hepatitis, atrophic gastritis with or without pernicious anemia (Biermer disease), intestinal infections, and malabsorption. In contrast to the major organ-specific autoimmune symptoms of APECED, the GI symptoms and their underlying pathogenesis are poorly understood. Yet isolated case reports and small series depict severe intestinal involvement in children, leading to malabsorption, multiple deficiencies, growth impairment, and possible death. Moreover, very few systematic studies of GI function with intestinal biopsies have been performed. GI symptoms may be the first manifestation of APECED, yet they may have various causes; effective treatment will therefore vary. We provide here an updated review of GI manifestations in APECED, including principles of diagnosis and therapy.