Background: APECED (Autoimmune Polyendocrinopathy Candidiasis Ectodermal Dystrophy) is a rare autosomal recessive disease characterised primarily by sequential immune-mediated destruction of endocrine tissues, chronic oral or mucocutaneous candidiasis and ectodermal disorders, including hypoplasia of dental enamel. Aim: This was to investigate the oral health and presence of enamel defects in a cohort of patients with APECED. Methods: 16 patients with APECED (mean age of 13.9 years) were matched for age and gender with healthy controls. A comprehensive medical, dental and drug history was recorded, followed by a clinical assessment of oral health which was determined by assessing periodontal treatment needs, prevalence of dental caries, erosion, fluorosis and enamel defects. The estimated time of the development of the enamel defects and the contemporaneous medical diagnosis were recorded. Results: Oral health of patients with APECED was poor compared with controls, with a higher prevalence of periodontal disease, caries and erosion. There was a significantly (P < 0.05) higher prevalence of enamel defects in the study group. The enamel defects were mostly hypoplastic in the form of pits, missing enamel and grooves. The enamel defects occurred in a chronological pattern. There was a strong association between the estimated time of defective enamel formation and a history of hypoparathyroidism. Gastrointestinal dysfunction and a history of chronic mucocutaneous candidiasis were also associated with the presence of enamel defects. Conclusion: The oral health of individuals with APECED was poor compared with controls with a higher prevalence of periodontal disease, caries, erosion and enamel defects. The enamel defects in the study population occurred in a chronological pattern and some were associated with a history of systemic disease during the period of tooth development.