- Inguinal hernia (HP:0000023): Protrusion of the contents of the abdominal cavity through the inguinal canal. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:325345)
- Epispadias (HP:0000039): Epispadias is a urogenital malformation characterized by the failure of the urethral tube to tubularize on the dorsal aspect. Unlike in hypospadias, where the meatus is on the ventral aspect, children with epispadias have a wide-open urethral plate on the dorsum. It is commonly seen as a component in the spectrum of bladder exstrophy-epispadias-complex. Isolated epispadias constitutes less than 10 percent of the total cases of epispadias. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:325345)
- Chordee (HP:0000041): A congenital anomaly of the penis characterized by ventral (i.e., downward), lateral, or ventrolateral curvature of the shaft and glans penis of more than 30 degrees. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:325345)
- Bifid scrotum (HP:0000048): Midline indentation or cleft of the scrotum. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:325345)
- Perineal hypospadias (HP:0000051): Hypospadias with location of the urethral meatus in the perineal region. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:325345)
- Micropenis (HP:0000054): Abnormally small penis. At birth, the normal penis is about 3 cm (stretched length from pubic tubercle to tip of penis) with micropenis less than 2.0-2.5 cm. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:325345)
- Abnormal clitoris morphology (HP:0000056): Any structural abnormality of the clitoris. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:325345)
- Abnormal labia morphology (HP:0000058): An anomaly of the labia, the externally visible portions of the vulva. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:325345)
- Ambiguous genitalia (HP:0000062): A genital phenotype that is not clearly assignable to a single gender. Ambiguous genitalia can be evaluated using the Prader scale: Prader 0: Normal female external genitalia. Prader 1: Female external genitalia with clitoromegaly. Prader 2: Clitoromegaly with partial labial fusion forming a funnel-shaped urogenital sinus. Prader 3: Increased phallic enlargement. Complete labioscrotal fusion forming a urogenital sinus with a single opening. Prader 4: Complete scrotal fusion with urogenital opening at the base or on the shaft of the phallus. Prader 5: Normal male external genitalia. The diagnosis of ambiguous genitalia is made for Prader 1-4. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:325345)
- Fused labia minora (HP:0000063): Fusion of the labia minora as a result of labial adhesions resulting in vaginal obstruction. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:325345)
- Gonadoblastoma (HP:0000150): The presence of a gonadoblastoma, a neoplasm of a gonad that consists of aggregates of germ cells and sex cord elements. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:325345)
- Abnormality of prenatal development or birth (HP:0001197): An abnormality of the fetus or the birth of the fetus, excluding structural abnormalities. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:325345)
- True hermaphroditism (HP:0010459): The presence of both ovarian and testicular tissues either in the same or in opposite gonads. Affected persons have ambiguous genitalia and may have 46,XX or 46,XY karyotypes or 46,XX/XY mosaicism. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:325345)
- Abnormality of the female genitalia (HP:0010460): Abnormality of the female genital system. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:325345)
- Abnormality of the male genitalia (HP:0010461): Abnormality of the male genital system. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:325345)
- Abnormal sex determination (HP:0012244): Anomaly of primary or secondary sexual development or characteristics. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:325345)
- Hyperpigmented genitalia (HP:0030258): Localized or generalized increased genital pigmentation. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:325345)
- Ovotestis (HP:0012861): A gonad that contains both ovarian follicles and testicular tubular elements. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:325345)
- Urogenital sinus anomaly (HP:0100779): A rare birth defect in women where the urethra and vagina both open into a common channel. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:325345)
These phenotypes are associated with the disease 46,XY ovotesticular difference of sex development (ORPHA:325345).