To evaluate the hypothesis of a common etiology for cryptorchidism and hypospadias, we conducted two case-control studies nested in a nationwide cohort in Sweden, using record linkage between the Inpatient and Birth Registries. Cases were 2,782 and 1,220 boys operated for cryptorchidism or hypospadias, respectively. Five matched controls per case were randomly selected. Pregnancy and perinatal data were prospectively recorded in the Birth Registry. Data were modeled through conditional logistic regression. Both cryptorchidism (odds ratio (OR) = 2.22) and hypospadias (OR = 2.75) were positively associated with other congenital malformations and inversely with maternal parity (OR = 0.77 and 0.52, respectively, for parity 4+ compared with primiparae). There is evidence that being born small-for-gestational-age and before the 33rd gestational week have a greater-than-additive effect with respect to both cryptorchidism (OR = 6.19 vs 1.72 expected) and hypospadias (OR = 4.39 vs 2.60 expected) compared with non-small-for-gestational-age boys born at term. Hypospadias was positively associated with severe preeclampsia (OR = 2.11). We conclude that the etiologies of the two conditions are partly shared.