The diagnosis of hypospadias has been made with both antenatal fetal ultrasonography , the diagnosis is generally made upon examination of the newborn infant.

A dorsal hood of foreskin and glandular groove are evident, but upon closer inspection, the prepuce is incomplete ventrally and the urethral meatus is noted in a proximally ectopic position. Rarely, the foreskin may be complete, and the hypospadias is revealed at the time of circumcision.

If hypospadias is encountered during neonatal circumcision, after the dorsal slit has been performed, the procedure should be halted, and the patient should be referred for urologic evaluation.

Proximal hypospadias is commonly associated with a bifid scrotum and penoscrotal transposition which the rugated scrotal skin begins lateral to the penis rather than in its normal posterior origin.