The present study represents the largest ever (425 controls; 421 cryptorchid; 109 hypospadias) case–control study to assess the role of fetal androgens and INSL3 in subsequent cryptorchidism and hypospadias, using second trimester amniotic fluid samples collected in Denmark as part of a national biobank (Jensen et al., 2012). Here, INSL3 is linked to hypospadias.