The aim of the present study was to examine the seasonality of hypospadias in Greece in an attempt to elucidate the aetiology. All boys born between 1991–1998, who underwent hypospadias repair at ‘Aghia Sophia’ Children's Hospital, Athens (n=542) were analysed. All Greek live-born males during the same period (population at risk; m=421,175) served as the controls. Seasonality by month of birth was evaluated with specific statistical tools. Meteorological parameters were also analysed. All tests yielded significant results, suggesting a simple harmonic prevalence pattern (highest/lowest: autumn, peak in October/spring, trough in April). Therefore, the first trimester of hypospadiac gestations coincides more frequently with winter. Meteorological parameters varied seasonally (maximal sunlight; air temperature in summer/minimal in winter, maximal rainfall in winter/minimal in summer) and were strongly associated pairwise. Hypospadiac birth prevalence follows a simple harmonic seasonal pattern and is associated with that of cryptorchidism in Greece. The coincidence of the first or third trimester of a potentially genetically influenced gestation with winter could lead to the phenotypic expression of hypospadias or cryptorchidism, respectively. The potential role of a cyclic-varied androgen-production stimulator, such as human chorionic gonadotrophin may be speculated. The seasonality of a common environmental factor acting directly/indirectly may contribute to these patterns, and possibly to the common pathogenesis of these congenital malformations.