- Bifid scrotum (HP:0000048): Midline indentation or cleft of the scrotum. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:227)
- Abnormality of the genitourinary system (HP:0000119): The presence of any abnormality of the genitourinary system. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:227)
- Bifid penis (HP:0100599): Two penile structures, separated from the tip to the base of the shaft. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:227)
- 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: Frequent (HP:0040282). (ORPHA:227)
- Anal atresia (HP:0002023): Congenital absence of the anus, i.e., the opening at the bottom end of the intestinal tract. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:227)
- Distal urethral duplication (HP:0008706). Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:227)
- Ectopic scrotum (HP:0030275): Scrotum in a position other than the usual position inferior to the base of the penis. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:227)
- Penoscrotal transposition (HP:0100600): A partial or complete positional exchange between the penis and the scrotum, with positioning of the scrotum superior to the penis. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:227)
- Inguinal hernia (HP:0000023): Protrusion of the contents of the abdominal cavity through the inguinal canal. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:227)
- 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: Occasional (HP:0040283). (ORPHA:227)
- 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:227)
- Ureteral duplication (HP:0000073): A developmental anomaly characterized by the presence of two, instead of one, ureter connecting a kidney to the bladder. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:227)
- Renal duplication (HP:0000075): A congenital anomaly of the urinary tract, in which the kidney is duplicated and is drained via two separate renal pelves and ureters. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:227)
- Horseshoe kidney (HP:0000085): A connection of the right and left kidney by an isthmus of functioning renal parenchyma or fibrous tissue that crosses the midline. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:227)
- Abnormal heart morphology (HP:0001627): Any structural anomaly of the heart. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:227)
- Atrial septal defect (HP:0001631): Atrial septal defect (ASD) is a congenital abnormality of the interatrial septum that enables blood flow between the left and right atria via the interatrial septum. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:227)
- Bladder exstrophy (HP:0002836): Eversion of the posterior bladder wall through the congenitally absent lower anterior abdominal wall and anterior bladder wall. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:227)
- Abnormal pubic bone morphology (HP:0003172): An anomaly of the the pubic bone, i.e., of the ventral and anterior of the three principal components (pubis, ilium, ischium) of the hip bone. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:227)
- Renal malrotation (HP:0004712): An abnormality of the normal developmental rotation of the kidney leading to an abnormal orientation of the kidney. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:227)
- Abnormal spermatogenesis (HP:0008669): Incomplete maturation or aberrant formation of the male gametes. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:227)
- Cloacal exstrophy (HP:0010475): Cloacal exstrophy is a severe anterior abdominal wall defect in which the two hemibladders are visible and are separated by a midline intestinal plate, an omphalocele, and an imperforate anus. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:227)
- Abnormality of the gastrointestinal tract (HP:0011024): An abnormality of the gastrointestinal tract. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:227)
- Gastrointestinal duplication (HP:0011140): A spherical hollow structure with a smooth muscle coat, lined by a mucous membrane, and attached to any part of the gastrointestinal tract, from the base of the tongue to the anus. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:227)
- Scoliosis (HP:0002650): The presence of an abnormal lateral curvature of the spine. Evidence: TAS. Frequency: Very rare (HP:0040284). (ORPHA:227)
- Hemivertebrae (HP:0002937): Absence of one half of the vertebral body. Evidence: TAS. Frequency: Very rare (HP:0040284). (ORPHA:227)
- Butterfly vertebrae (HP:0003316): A butterfly vertebra (sagittal cleft vertebra or anterior rachischisis) is a sagittal defect in the vertebral body caused by failure of fusion of the two lateral chondrification centers during embryogenesis. The name is based on the appearance of the two hemivertebrae emerging as butterfly wings from the central cleft on x-ray. Evidence: TAS. Frequency: Very rare (HP:0040284). (ORPHA:227)
- Rectoperineal fistula (HP:0004792): The presence of a fistula between the perineum and the rectum. Evidence: TAS. Frequency: Very rare (HP:0040284). (ORPHA:227)
- Duplicated colon (HP:0005223). Evidence: TAS. Frequency: Very rare (HP:0040284). (ORPHA:227)
- Absent thumb (HP:0009777): Absent thumb, i.e., the absence of both phalanges of a thumb and the associated soft tissues. Evidence: TAS. Frequency: Very rare (HP:0040284). (ORPHA:227)
These phenotypes are associated with the disease Diphallia (ORPHA:227).