Epispadias is caused by malformation of the embryonic genital tubercle and cloacal membrane sometime in the 5th or 6th week of pregnancy. It is not related to hypospadias, which is thought to be a hormonally moderated defect of penile formation and closure of the urethral plate, which takes place about 8 weeks after conception.
Estimates are that epispadias with exstrophy occurs about once every 30,000 births, isolated epispadias without exstrophy in males about once in 120,000, and isolated epispadias in females about once in 500,000.