The current study was aiming to report the prevalence of suboptimal vitamin D status among schoolchildren in Greece and investigate the role of sex, urbanisation and seasonality on vitamin D status. A sample of 2386 schoolchildren (9-13 years old) from four distinct prefectures was examined. The prevalence of 25-hydroxyvitamin D (25(OH)D) concentration <30 and <50 nmol/l (vitamin D deficiency and insufficiency respectively) was 5·2 and 52·5 %, respectively. Girls had a higher prevalence of 25(OH)D<30 (7·2 v. 3·2 %) and 50 nmol/l (57·0 v. 48·0 %) than boys (P<0·001). The highest prevalence rates of 25(OH)D<30 and 50 nmol/l (9·1 and 73·1 %, respectively) were observed during spring (April to June), whereas the lowest (1·5 and 31·9 %, respectively) during autumn (October to December). The prevalence of 25(OH)D<50 nmol/l was higher in urban/semi-urban than rural regions, particularly during spring months (74·6 v. 47·2 %; P<0·001). Female sex, urban/semi-urban region of residence and spring months were found to increase the likelihood of vitamin D deficiency and insufficiency, with the highest OR observed for spring months (7·47; 95 % CI 3·23, 17·3 and 5·14; 95 % CI 3·84, 6·89 for 25(OH)D<30 and 50 nmol/l respectively). In conclusion, despite the southerly latitude, the prevalence of low vitamin D status among primary schoolchildren in Greece is comparable to or exceeds the prevalence reported among children and adolescents on a European level. Sub-populations at highest risk are girls in urban/semi-urban areas during spring months, thus indicating the need for effective initiatives to support adequate vitamin D status in these population groups.