
Aposthia is a rare congenital condition in humans, in which the foreskin of the penis is missing.

A bifid penis is a rare congenital defect where two genital tubercles develop.

Chordee is a condition in which the head of the penis curves downward or upward, at the junction of the head and shaft of the penis. The curvature is usually most obvious during erection, but resistance to straightening is often apparent in the flaccid state as well. In many cases but not all, chordee is associated with hypospadias. This is not the same condition as Peyronie's disease, which involves curvature of the shaft of the penis most commonly due to injury during adult life.

Diphallia, penile duplication (PD), diphallic terata, or diphallasparatus, is an extremely rare developmental abnormality in which a person is born with two penises. The first reported case was by Johannes Jacob Wecker in 1609. Its occurrence is 1 in 5.5 million boys in the United States.

An epispadias is a rare type of malformation in which the urethra ends, in males, in an opening on the upper aspect of the penis, and in females when the urethra develops too far anteriorly. It occurs in around 1 in 120,000 male and 1 in 500,000 female births.

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 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 should have made the urethra extends from the meatus to the tip of the glans; this tissue is called the urethral plate.

Micropenis is an unusually small penis. A common criterion is a dorsal erect penile length of at least 2.5 standard deviations smaller than the mean human penis size, or smaller than about 7 cm for an adult when compared with an average erection of 12.5 cm (5 in). The condition is usually recognized shortly after birth. The term is most often used medically when the rest of the penis, scrotum, and perineum are without ambiguity, such as hypospadias. Micropenis occurs in about 0.6% of males.

Persistent Müllerian duct syndrome (PMDS) is the presence of Müllerian duct derivatives in what would be considered a genetically and otherwise physically normal male animal by typical human based standards. In humans, PMDS typically is due to an autosomal recessive congenital disorder and is considered by some to be a form of pseudohermaphroditism due to the presence of Müllerian derivatives.

Polyorchidism is the incidence of more than two testicles. It is a very rare congenital disorder, with fewer than 200 cases reported in medical literature and six cases in veterinary literature.

Webbed penis is an acquired or congenital condition in which the scrotal skin extends onto the ventral penile shaft. The penile shaft is buried in scrotum or tethered to the scrotal midline by a fold or web of skin. The urethra and erectile bodies are usually normal. Webbed penis is usually asymptomatic, but the cosmetic appearance is often unacceptable. This condition may be corrected by surgical techniques.