Objectives: To evaluate prevalence of vitamin D deficiency and its associated factors in southern Iranian children. Design: Cross-sectional study. Anthropometric and pubertal characteristics were assessed by a trained physician. Physical activity and sun exposure were evaluated using standard questionnaires. Body composition measurements were performed using dual-energy X-ray absorptiometry. Serum Ca, P alkaline phosphatase and 25-hydroxyvitamin D (25(OH)D) were assessed in all children. Statistical analysis was done using the statistical software package IBM SPSS Statistics 18·0. Subjects: Iranian children (n 477) aged 9-18 years. Setting: Fars Province, Iran, 2011. Results: Of the children, 81·3 % were 25(OH)D deficient. There was no significant difference in 25(OH)D concentration between boys and girls (P = 0·3). 25(OH)D concentration was associated with BMI (r = − 0·1, P = 0·02), pubertal status (r = − 0·08, P = 0·04) and sun exposure (r = 0·10, P = 0·04). Fat mass index was associated with 25(OH)D concentration (r = − 0·13, P = 0·03), but not lean mass index (P = 0·86). In multiple regression analysis with adjustment for confounding factors, age and puberty were found to be independently associated with 25(OH)D concentration (P = 0·008 and P = 0·006); there was a significant correlation between exercise and 25(OH)D concentration after adjustment for either BMI (P = 0·01) or fat mass index (P = 0·02). Conclusions: 25(OH)D deficiency is highly prevalent among children in the south of Iran. It is related to insufficient sun exposure, low physical activity, advancing age and pubertal stage. Measures should be taken to improve the health of southern Iranian children in this critical age group by preventing 25(OH)D deficiency.