Congenital Urogenital Malformations

oPatientPlus articles are written by UK doctors and are based on research evidence, UK and European Guidelines. They are designed for health professionals to use, so you may find the language more technical than the condition leaflets.

The kidney is the most common site of congenital abnormalities. Some cause no problems but many result in impaired renal function. Renal malformations are often associated with other congenital defects - eg, a grossly deformed pinna with ipsilateral abnormalities of the facial bones.

  • Renal agenesis:
    • Virtually always unilateral.
    • Kidney is either absent or undeveloped.
    • It usually causes no symptoms and is found incidentally.
  • Renal hypoplasia:
    • This may appear as one small kidney with the other one larger than normal.
    • Small kidneys also have small arteries and are associated with hypertension requiring nephrectomy.
  • Supernumerary kidneys:
    • Third kidney is very rare and not to be confused with the relatively common unilateral duplication of the renal pelvis.
  • Renal dysplasia and multicystic kidney:
    • Multicystic kidney of the newborn is normally seen in only one kidney as an irregularly lobulated mass of cysts and usually absent or atretic ureter.
    • Frequently associated with contralateral abnormalities, especially ureteropelvic junction obstruction.
    • Dysplasia of the renal parenchyma is seen with urethral obstruction or reflux present early in pregnancy, or obstructed ureter.
  • Adult polycystic kidney disease.
  • Infantile polycystic kidneys.
  • Simple (solitary) renal cyst:
    • This may be inherited or acquired.
    • Significant renal damage is rare and usually only requires continuous follow-up.
  • Renal fusion:
    • Prevalence is 1 in 1,000 people.
    • The most frequent abnormality seen is a horseshoe kidney containing two excretory systems and two ureters.
    • They are usually asymptomatic but are prone to obstruction.
  • Ectopic kidney:
    • In simple ectopy, the kidney does not ascend properly and is found in the pelvis or over the brim.
    • It is prone to obstruction and infection.
    • Less common is crossed ectopy without fusion. The kidney then lies on the opposite side and is not attached to the normally placed kidney.
    • Abnormal rotation: this rarely leads to renal disease.
  • Medullary sponge kidney.
  • Potter's syndrome.

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These are relatively common and range from complete absence to duplication of the ureter.

  • Ureteral atresia:
    • The ureter may be absent or fail to extend to the bladder (therefore with a blind ending).
    • It is associated with ipsilateral absent or multicystic kidney.
    • Bilateral atresia is incompatible with life. Unilateral atresia is usually asymptomatic but may cause hypertension.
  • Duplication of the ureter:
    • This is one of the most common congenital malformations of the urinary tract, with duplication found in 0.9% of a series of autopsies.
    • It is more common in females and is often bilateral.
    • It is often asymptomatic but commonly presents with persistent or recurrent urinary tract infections.
  • Ureterocele:
    • This is a sacculation of the bladder end of the ureter that can occur either in the bladder or ectopically.
    • It is much more common in girls than in boys.
    • In 10% of cases it is bilateral.
    • It may be asymptomatic or cause obstruction or incontinence or infection.
  • Ectopic urethral orifice:
    • This usually occurs with ureterocele and duplication of the ureter but single ectopic ureters are seen.
    • Boys may present with epididymitis, as the ureter drains directly into the vas deferens or seminal vesicle.
    • Girls normally present with incontinence with continual dribbling despite normal voiding.
  • Obstruction of the ureteropelvic junction:
    • This is a common congenital abnormality of the ureter, seen more often in boys than in girls.  Most cases are unilateral and usually on the left.
    • It is nearly always caused by a kink in the ureter where it meets the dilated renal pelvis.
    • It can be diagnosed in utero.
    • In children, it normally presents with pain and vomiting.
  • Obstructed mega-ureter:
    • This is caused by obstruction at the ureterovesical junction.
    • It is four times more common in boys than in girls and is often bilateral.
    • Often, it is associated with absent or dysplastic contralateral kidney.
    • It is usually discovered during prenatal ultrasound.
    • It frequently presents with haematuria, with symptoms of infection and abdominal pain.
  • Bladder exstrophy:
    • This is absence of the anterior wall of the bladder, with ureters delivering urine into the lower abdomen.
    • It is associated with other abnormalities, especially epispadias.
    • It requires surgical reconstruction.
  • Persistent urachus:
    • This may appear as a draining umbilical sinus and can become infected.
  • Contracture of the bladder neck:
    • This is a common cause of reflux, bladder diverticula and irritable bladder.
  • Apenia:
    • Congenital absence of the penis is very rare.
    • More than 50% of patients have associated genitourinary anomalies - eg, cryptorchidism, renal agenesis and dysplasia.
  • Megalopenis:
    • The penis enlarges rapidly in childhood due to a high level of production of testosterone.
  • Micropenis:
    • This is a small but otherwise normally formed penis with a stretched length of less than 2.5 standard deviation below the mean. It is important to distinguish miscropenis from buried and webbed penis, which is usually of normal size. The most common aetiologies are:
      • Hypogonadotropic hypogonadism: impaired secretion of gonadotrophin-releasing hormone (GnRH) by the hypothalamus occurs in some hypothalamic dysfunctions - eg, Kallmann's syndrome, Prader-Willi syndrome.
      • Hypergonadotropic hypogonadism: the testes are functionally impaired - eg, gonadal dysgenesis.
      • Idiopathic micropenis: there is normal hypothalamic-pituitary-testicular endocrine function.
  • Urethral stricture:
    • This is uncommon; the two most common sites are the fossa navicularis and the membranous urethra.
    • Severe cases can result in damage to the bladder and hydronephrosis due to back pressure of urine.
  • Posterior urethral valves:
    • A relatively frequent obstructive lesion in male neonates and infants.
    • They are found at the distal prostatic urethra and mucosal folds, looking like thin membranes and causing varying degrees of obstruction when attempting to urinate.
    • Boys usually present with a poor, intermittent, dribbling stream with frequent infection.
  • Hypospadias:
    • Urethral meatus is found on the underside of the penis.
    • It occurs in around 1 in 300 male births.
    • Around 7% of patients have an additional family member with hypospadias.
    • Most cases occur on the distal penis or corona.
    • Young children seldom report symptoms but older children and adults may complain of difficulty in directing the urinary stream, and of spraying.
    • Around 10% of cases also have cryptorchidism.
    • 9-15% of cases also have an open processus vaginalis or inguinal hernia.
  • Epispadias:
    • This consists of a defect of the dorsal wall of the urethra.
    • The extent of the defect can vary from a mild glandular defect to complete defects, as are observed in bladder exstrophy and/or diastasis of the pubic bones.
    • Epispadias occurs in 1 in 120,000 males and 1 in 450,000 females.
    • The urethra is displaced dorsally so that it opens on to the top of the penis in males.
    • Females have a bifid clitoris and separation of the labia.
    • Incontinence is a common problem.
  • Distal urethral stenosis:
    • This occurs in young girls with enuresis with slow and interrupted stream and recurrent infection.
    • It is associated with secondary spasm of the external sphincter.
  • Labial fusion:
    • Fused labia minora can present with recurring urinary infection as a result of obstruction to the urine flow.
  • Clitoral hypertrophy:
    • This is caused by fetal exposure to androgens, usually caused by congenital deficiencies of adrenal enzymes of cortisol synthesis.
    • Rarely, it may also be due to in utero exposure to progestational agents or idiopathic virilisation.
  • Hypogonadism:
    • Small testes with lack of development of secondary sexual characteristics, lack of libido and potency.
    • Characteristically, patients are tall with long extremities.
    • It is also associated with Klinefelter's syndrome.
    • It is also associated with physiological problems and low intelligence.
  • Ectopy and cryptorchidism:
    • Ectopy: the testis has not followed the normal path of descent. By far the most common site is superficial inguinal.
    • Cryptorchidism: testicular descent is arrested. At 1 year of age, nearly 1% of all full-term male infants have cryptorchidism, which is the most common congenital anomaly affecting the genitalia of newborn male infants.[1] The most useful classification of cryptorchidism is into palpable and non-palpable testes, and clinical management is decided by the location and presence of the testes:
      • Retractile testes require only observation.
      • Bilateral, non-palpable testes and any suggestion of sexual differentiation problems (eg, hypospadias) require urgent, mandatory endocrinological and genetic evaluation.
      • Surgical orchidolysis and orchidopexy should be concluded at the age of 12 months, or 18 months at the latest.
  • Spermatocele:
    • This is a painless cystic mass found just above or posterior to the testis.
    • They are mostly <1 cm in diameter and usually require no therapy.
  • Varicocele:
    • These are unusual in boys aged under 10 years and are more frequent at the beginning of puberty. They occur in around 14-20% of adolescents.
    • They appear mostly on the left side (78-93% of cases).
    • They are caused by dilatation of the pampiniform plexus (spermatic venous plexus).
    • Fertility problems arise in around 20% of adolescents with a varicocele.
    • Surgery is recommended for:
      • Varicocele associated with a small testis.
      • Additional testicular condition affecting fertility.
      • Pathological sperm quality (in older adolescents).
      • Bilateral palpable varicocele.
      • Symptomatic varicocele.[1] 
  • Hydrocele:
    • This is an excess of fluid between the two layers of the tunica vaginalis in young boys.
    • It presents as a cystic mass which is often more tense at night.
    • In the majority of infants, surgical treatment of hydrocele is not indicated within the first 12-24 months, as they usually resolve spontaneously.
    • Early surgery is indicated if there is suspicion of a concomitant inguinal hernia or underlying testicular pathology.[1] 
  • Turner syndrome.
  • Other syndromes of gonadal dysgenesis:
    • These range from bilateral streaks or bilateral dysgenetic testes to apparently normal testes.
    • They may be asymmetrical - eg, streaked one side, normal the other. This is mixed gonadal dysgenesis.
  • The formerly called 'intersex disorders' have been changed to 'disorders of sex development' (DSD).[2].
  • This classification has arisen because of advances in knowledge of the molecular genetic causes of abnormal sexual development, controversies inherent to clinical management and ethical issues.
  • Findings in a newborn suggesting the possibility of DSD include (adapted from the American Academy of Pediatrics):
    • Apparent male:
      • Severe hypospadias associated with bifid scrotum.
      • Undescended testis/testes with hypospadias.
      • Bilateral non-palpable testes in a full-term apparently male infant.
    • Apparent female:
      • Clitoral hypertrophy of any degree, non-palpable gonads.
      • Vulva with single opening.
    • Indeterminate:
      • Ambiguous genitalia.
      • Any neonate presenting with ambiguous genitalia is an emergency since salt-losing in a 46XX CAH girl can be fatal.

See the separate article on Ambiguous Genitalia. Management of intersex conditions is complex and involves a person's gender identity, gender role behavior, sexual orientation, sexual functioning, and psychological adjustment.[3] 

Further reading & references

  1. Guidelines on Paediatric Urology; European Association of Urology (Mar 2013)
  2. Lee PA, Houk CP, Ahmed SF, et al; Consensus statement on management of intersex disorders. International Consensus Pediatrics. 2006 Aug;118(2):e488-500.
  3. Calleja-Agius J, Mallia P, Sapiano K, et al; A review of the management of intersex. Neonatal Netw. 2012 Mar-Apr;31(2):97-103. doi: 10.1891/0730-0832.31.2.97.

Disclaimer: This article is for information only and should not be used for the diagnosis or treatment of medical conditions. EMIS has used all reasonable care in compiling the information but make no warranty as to its accuracy. Consult a doctor or other health care professional for diagnosis and treatment of medical conditions. For details see our conditions.

Original Author:
Dr Colin Tidy
Current Version:
Peer Reviewer:
Dr Helen Huins
Last Checked:
07/07/2013
Document ID:
1998 (v22)
© EMIS