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Evidence suggests that there is geographical variation in the birth prevalence of both cryptorchidism and hypospadias. The aim was to determine if there is evidence of spatial heterogeneity in the prevalence of these conditions and to test the hypothesis that environmental factors may contribute to aetiology.A population-based dataset of cryptorchidism and hypospadias cases was constructed from the hospital episodes statistics that covered the Northern Region of England and assigned to a small area based on the residential address at time of admission. Expected numbers of cases for each small area were computed. The ratio of observed to expected cases was determined for each small area and analysed with respect to both geographical heterogeneity and small area level socio-economic deprivation. The Potthoff–Whittinghill method was used to determine if there was localized spatial clustering of cases.There was statistically significant spatial clustering for cases of both cryptorchidism [estimated Extra-Poisson Variation (EPV) = 0.14; 95% CI, 0.03–0.25] and hypospadias (EPV = 0.17; 95% CI, 0.05–0.28). In addition, increased prevalence was associated with lower levels of deprivation for hypospadias (P = 0.06), but there was no such relationship for cryptorchidism (P = 0.61).The finding of localized spatial heterogeneity in the prevalence of cryptorchidism and hypospadias is consistent with the involvement of a spatially varying environmental risk factor. The apparent social patterning of hypospadias is likely to reflect an association with lifestyle and other factors which underpin social variation in health. However, there also remains a possibility that these findings may be due to variability in ascertainment of cases.