Hypospadias is a common variation in fetal development of the penis in which the urethra does not open from its usual location in the head of the penis. It is the second-most common birth abnormality of the male reproductive system, affecting about one of every 250 males at birth. Roughly 90% of cases are the less serious distal hypospadias, in which the urethral opening (the meatus) is on or near the head of the penis (glans). The remainder have proximal hypospadias, in which the meatus is all the way back on the shaft of the penis, near or within the scrotum. Shiny tissue that typically forms the urethra instead extends from the meatus to the tip of the glans; this tissue is called the urethral plate.

In most cases, the foreskin is less developed and does not wrap completely around the penis, leaving the underside of the glans uncovered. Also, a downward bending of the penis, commonly referred to as chordee, may occur. Chordee is found in 10% of distal hypospadias and 50% of proximal hypospadias cases at the time of surgery. Also, the scrotum may be higher than usual on either side of the penis (called penoscrotal transposition).

The cause of hypospadias is unknown. It most often occurs by itself, without other variations, although in about 10% of cases it may be part of an intersex condition or a medical syndrome with multiple abnormalities.

The most common associated difference is an undescended testicle, which has been reported in around 3% of infants with distal hypospadias and 10% with proximal hypospadias. The combination of hypospadias and an undescended testicle sometimes indicates a child has an intersex condition, so additional testing may be recommended to make sure the child does not have congenital adrenal hyperplasia with salt wasting or a similar condition where immediate medical intervention is needed. Otherwise no blood tests or X-rays are routinely needed in newborns with hypospadias.

Hypospadias can be a symptom or indication of a difference in sex development or an intersex condition, but some consider that the presence of hypospadias alone is not enough to classify someone as a person with a difference/variation in sex development or as intersex. In most cases, hypospadias is not associated with any other condition. Hypospadias is however itself recognized as an intersex condition by several intersex rights activist groups, who consider the repositioning of a working urethra on a child too young to consent to be a human rights violation.