A rafe birth defect
Cloacal Exstrophy* is a rare birth defect involving the pelvic area that is termed a malformation sequence and involves the cloaca** and occurs once in every 250000 births. While it can affect girls or boys, in boys, they are typically born without a penis and/or other defects.
This can be so severe that it usually makes adequate reconstruction of the male genitalia difficult if not impossible, and gender reassignment has been performed over the past few decades with many boys born without a penis being converted surgically into females soon after birth. Their diminished phalluses were removed and reconstructed as vaginas; their parents encouraged to raise them as girls, but this has had unfortunate psychological consequences.
Cloacal Exstrophy is different from Cryptorchidism, a medical term referring to absence from the scrotum of one or both testes. This usually represents failure of the testis to move, or "descend," during fetal development from an abdominal position, through the inguinal canal, into the ipsilateral scrotum. About 3% of full-term and 30% of premature infant boys are born with at least one undescended testis, making cryptorchidism the most common birth defect of male genitalia. However, most testes descend by the first year of life (the majority within three months), making the true incidence of cryptorchidism around 1% overall.
* Exstrophy refers to the eversion of a hollow organ at birth (from the Greek ex, out, + strophe, a turning). In exstrophy of the cloaca, an area of the intestine is interposed between two separate areas of the bladder.
** A cloaca is a common passageway for feces, urine and reproduction. During human embryogenesis (development), there is for a time a cloaca. The far end of a structure called the hindgut is the cloaca before it divides to form a rectum, a bladder, and genitalia.