Background Strong evidence for a causal role of environmental factors in a congenital anomaly is still difficult to produce. The collection of statistical data is crucial for gaining a better understanding of the epidemiology and pathophysiology of these anomalies. We aimed to evaluate spatial variations in hypospadias in our region, taking into account of clinical data, and evaluate association to socio-economic and ecological data. Methods All boys with hypospadias born in northern France and seen in Lille University Medical Center (Lille, France) between 1999 and 2012 were included in the analysis. We retrospectively collected geographic data, clinical data (especially known confounding factors associated with an elevated risk of hypospadias), and demographic, socio-economic and ecological data. We analyzed the whole study population and then the subset of boys lacking confounding factors. Results The study sample of 975 cases of hypospadias was characterized by significant spatial heterogeneity (p<0.005) and autocorrelation (p<0.001). We detected two high-incidence clusters that differed with regard to their land use. After the exclusion of 221 patients with confounding factors, two high-incidence clusters with significant disease risks (1.65 and 1.75, respectively; p<0.001) and a significant difference in land use (p<0.001) again appeared. The first cluster contained a higher median [interquartile range] proportion of artificialized land (0.40 [0.22;0.47]) than the remaining “neutral areas” (0.19 [0.08;0.53]) did (p<0.001). Conversely, the second cluster contained a higher median proportion of rural land (0.90 [0.78;0.96]) than the “neutral areas” (0.81 [0.47;0.92]) did (p<0.001). The median deprivation index was significantly lower in the urban cluster (0.47 [0.42;0.55]) and significantly higher in the rural cluster (0.69 [0.56;0.73]) (p<0.001). Conclusions Our results evidenced the heterogeneous spatial distribution of cases of hypospadias in northern France. We identified two clusters with different environmental and social patterns – even after the exclusion of known confounding factors.