Penis & scrotum


Congenital anomalies

Last author update: 1 May 2010
Last staff update: 14 March 2022

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PubMed Search: Congenital anomalies[TIAB] penis

Alcides Chaux, M.D.
Antonio L. Cubilla, M.D.
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Cite this page: Chaux A, Cubilla AL. Congenital anomalies. website. Accessed April 15th, 2024.
  • Agenesis of penis caused by failure in embryologic development of genital tubercle
  • Very rare, incidence of 1 per 10 million male births; < 100 cases reported
  • Associated with other GU abnormalities and with musculoskeletal and cardiopulmonary defects
  • Can classify based on site of urethral meatus (J Urol 1989;141:589)
  • Case reports: associated with urethrorectal fistula (Saudi J Kidney Dis Transpl 2008;19:435), various anomalies (J Pediatr Surg 2010;45:E13)
Chordae (chordee)
  • Fibrous band associated with hypospadias or epispadias that causes bending of penis
Concealed penis
  • Also called hidden or buried penis
  • Penis is normally developed but hidden under fat in suprapubic region, scrotum, perineum and thigh
  • May be complication of circumcision
  • In adults, surgical repair may be complicated (J Sex Med 2009;6:876)
  • Duplication of penis
  • Occurs in 1 per 5 million male births
  • Associated with hypospadias, bifid scrotum, bladder duplication (Cir Pediatr 2008;21:235) and renal agenesis
  • Urethra opens onto dorsal surface of penis
  • Very rare, incidence of 1/300,000 male births
  • Part of exstrophy-epispadias complex (Orphanet J Rare Dis 2009;4:23)
  • Not related to hypospadias (has a different embryologic defect)
  • Penopubic epispadias (opening in penopubic junction) is most common, associated with urinary incontinence
  • Treatment is surgical
  • Most common congenital abnormality of male external genitalia other than cryptorchidism
  • Urethra opens onto ventral surface of penis or scrotum
  • 3 - 5/1000 live male births
  • Due to failure of fusion of urethral folds; may be due to mutations in MAMLD1 (CXorf6) gene (Horm Res 2009;71:245)
  • Urethral opening is usually near glans
  • Hypospadias and epispadias are associated with abnormal descent of testes, urinary tract malformations, obstruction, urinary tract infections and possibly infertility if orifices are near base of penis
  • Treatment is usually surgical unless hypospadias is minor (eMedicine: Hypospadias [Accessed 28 March 2018])

Classified by location of opening of meatus (see first clinical image below):
  • A: anterior (inferior surface of glans)
  • B: coronal (in balanopenile furrow)
  • C: distal third of shaft
  • D: penoscrotal (at base of shaft in front of scrotum)
  • E: scrotal (on scrotum or between the genital swellings)
  • F: perineal (behind scrotum or genital swellings)
Clinical images

Images hosted on other servers:


Epispadias: male baby

Proximal shaft


43 year old man with median raphe cyst

Lateral curvature
  • Due to hypo / hyperplasia of one corpora cavernosa
  • Surgical treatment is often effective (J Urol 2008;179:1495)
Median raphe cysts
  • Relatively common
  • Due to anomalies in development of urethral groove, trapped epithelial cells or migration of epithelial cells after closure of genital folds
  • Usually in foreskin or glans; may also be present in frenulum
  • Lined by squamous, columnar, mucus producing, apocrine-like or distal urethra type epithelium
  • Case report: 43 year old man with an asymptomatic nodule on glans (Dermatol Online J 2005;11:37)
Microscopic (histologic) images

Images hosted on other servers:

Median raphe cysts:

Pseudostratified columnar epithelium

Single larger mucinous cell

Cyst lining cells are CK7+

  • Fibrous tissue surrounding corpus spongiosum or short urethra causes rotational defect of penile shaft
  • Isolated neonatal torsion occurs in 27%, usually to left (J Pediatr Urol 2007;3:495)
  • Can be surgically corrected in adults, although patients often tolerate it without complaint (J Sex Med 2008;5:735)
Webbed penis
  • Scrotal skin extends to ventral portion of penis and hides it
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