- Abnormal morphology of female internal genitalia (HP:0000008): An abnormality of the female internal genitalia. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:2138)
- Abnormal male internal genitalia morphology (HP:0000022): An abnormality of the male internal genitalia. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:2138)
- Cryptorchidism (HP:0000028): Testis in inguinal canal. That is, absence of one or both testes from the scrotum owing to failure of the testis or testes to descend through the inguinal canal to the scrotum. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:2138)
- Small scrotum (HP:0000046): Apparently small scrotum for age. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:2138)
- Hypospadias (HP:0000047): Abnormal position of urethral meatus on the ventral penile shaft (underside) characterized by displacement of the urethral meatus from the tip of the glans penis to the ventral surface of the penis, scrotum, or perineum. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:2138)
- Bifid scrotum (HP:0000048): Midline indentation or cleft of the scrotum. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:2138)
- 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:2138)
- Abnormality of the uterus (HP:0000130): An abnormality of the uterus. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:2138)
- Decreased fertility (HP:0000144). Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:2138)
- Polycystic ovaries (HP:0000147). Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:2138)
- Hypoplasia of penis (HP:0008736). Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:2138)
- 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:2138)
- Abnormal scrotal rugation (HP:0012856): Anomaly of the folded ridges (wrinkles) of skin of the scrotum. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:2138)
- 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:2138)
These phenotypes are associated with the disease 46,XX ovotesticular difference of sex development (ORPHA:2138).