We evaluated the prevalence of autoimmune thyroiditis in a random sample of 1188 schoolchildren aged 8–13 years with normalized iodine intake in the Islamic Republic of Iran. The prevalence of goitre was 39.6%; the majority had palpable but non-visible goitre. Of a subsample of 500 children, median urinary iodine excretion (18/8 µg/dL) indicated normal iodine intake. Thyroid peroxidase (TPO) antibody was positive in 3.7% of children and was significantly correlated with the prevalence of goitre and hypothyroidism. No correlation was seen between urinary iodine excretion and positive TPO antibody, mean TPO antibody, hypothyroidism or prevalence of goitre. Autoimmune thyroiditis explains some cases of goitre but other goitrogenic factors need to be evaluated.