During the 8 – 20 weeks of pregnancy, the urogenital tract develops and this development is regulated by certain hormones like sex hormones e.g. androgens and progesterone.
Any defect in the secretion of these hormones or inability to respond to them affects the development of the urogenital tract.
A study has shown that boys born through in vitro fertilization are more at risk of developing hypospadias than normally born boys. And this is thought to be due to the amount of progesterone administered to the mother then.