To study if parental subfertility is related to the occurrence of the male genital anomalies, cryptorchidism and hypospadias. Population-based cohort study. Not applicable. A total of 80,220 singleton boys and their mothers from the Danish National Birth Cohort and the Aarhus Birth Cohort. None. The two congenital anomalies; cryptorchidism and hypospadias, registered within the Danish National Patient Register up until December 31,2012. By means of Cox regression analyses, we found no associations between waiting time-to-pregnancy (TTP) and cryptorchidism or hypospadias among those who conceived spontaneously. The highest hazard ratio for cryptorchidism was seen among boys of couples with a TTP>12months who conceived after fertility treatment (adjusted hazard ratio [aHR] 1.19, 95% confidence interval 0.92-1.55). For hypospadias, we found that boys of couples with a TTP>12months who conceived after fertility treatment, had a 71% higher risk of hypospadias (aHR 1.71, [95% confidence interval 1.24-3.36]) as compared with boys of couples with a TTP<5months. The findings from this study showed that boys of couples with TTP>12months who conceived after fertility treatment, had a higher occurrence of hypospadias than boys conceived spontaneously of couples with a short TTP. Among those who conceived spontaneously, TTP was not associated with hypospadias or cryptorchidism. These findings indicate that fertility treatment or severity of subfertility is related to hypospadias.