What are the causes of Hypospadias? Depending on the boy and the conditions, there are relatively 4 to 5 causes doctors have come up with that causes hypospadias in some boys. The reasons are as follows Genetic disorder- hypospadias is associated with some genetic syndrome where it is more likely to happen to a boy if his brother or father was born with it. Fertility treatment or issues-hypospadias may happen to a boy whose mother may have used medicines or hormone therapy to help them get pregnant. The age and weight of the mother-if the mother is over age i.e. 35 or overweight then there are more chances of the baby will be born with hypospadias. A baby boy will be more likely to be born with hypospadias if a mother even has diabetes before the pregnancy. If a mother is more exposed to pesticides or smoking or extreme alcohol then the baby boy may have hypospadias If a baby is premature this may cause hypospadias.