Congenital Anomalies of the Kidneys and Urinary Tract: A Neonatal Factsheet

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CAKUT drives 40–50% of paediatric end-stage renal disease. A neonatal factsheet on reflux, obstruction, dysplasia and how to protect the nephrons you have.

Factsheet Nephrology & Urology Neonatal

Reference sheet for the congenital kidney and urinary tract anomalies a neonatal team meets most often — what each one is, what the antenatal scan shows, what to do in the first days, and which numbers predict what happens later.

The bottom line

Whatever the anomaly, the postnatal job is the same four things: establish urine drainage, prevent urinary tract infection, protect the nephrons that formed, and get nephrology and urology involved before problems declare themselves. Nephron mass is finite from 34 weeks onward — none of it grows back.4

40–50% of paediatric end-stage renal disease worldwide traces back to a congenital anomaly2
4–100 per 10,000 individuals — estimated prevalence range across studies1
10–25% attributable to an identifiable genetic disorder, often with extrarenal features1

Because a quarter of cases are genetic and those cases frequently come with developmental delay, congenital heart disease, endocrine disruption or immunodeficiency, a congenital renal anomaly is itself a reason to consider genetic evaluation. Affected infants are also more likely to be born preterm and carry higher morbidity and mortality.1

01 The developmental clock

Every anomaly below is a failure at a datable point in a sequence, which is why the timeline is worth holding in your head rather than looking up.

From cervical nephrotomes to a finished kidney
Weeks 1–4Pronephros — a vestigial set of 7 to 10 nephrotomes in the cervical region, gone by the end of week four.3
Weeks 4–8Mesonephros — excretory tubules in an S-shaped loop, each with a glomerulus and Bowman capsule proximally. Mostly involutes in the second month; remnants near the gonads become the vas deferens in males.4
Week 5 onwardMetanephros, the definitive kidney. The wolffian duct swells into the ureteric bud and invades the metanephric mesenchyme; reciprocal signalling drives the branching that becomes collecting ducts, major and minor calyces.4
Nephron assemblyComma-shaped bodies become S-shaped bodies. The caudal pole becomes glomeruli, the cephalic portion the tubules. The kidney ascends from pelvis toward the thoracolumbar region, its blood supply handed off progressively to more cephalad aortic vessels.4
Weeks 4–7The cloaca divides into a ventral urogenital sinus and a dorsal anorectal canal. The urogenital sinus goes on to form bladder and urethra; ureteric orifices migrate cephalad and the mesonephric ducts enter the prostatic urethra to form the trigone.4
34 weeksNephrogenesis complete — roughly 800,000 to 1.2 million nephrons per kidney, and no more after that.4

02 When the tract is dilated

Dilatation is the commonest reason a kidney gets referred to you, and it has three usual explanations: urine going the wrong way, a hold-up at the pelvis, or a blocked outlet.

Vesicoureteral reflux — urine going backwards

Retrograde flow from bladder to upper tract, caused by aberrant insertion of the ureter into the bladder wall.34 Incidence sits between 0.4% and 1.8%,5 and around 30% to 40% of infants presenting with urinary tract infection turn out to have it.6

Primary reflux comes from a short intravesical ureteric segment that fails to close the orifice properly, and can improve with growth. Secondary reflux follows bladder outlet obstruction and tends to be bilateral. (mechanism, review consensus)

Voiding cystourethrography is the diagnostic standard.6

Ureteropelvic junction obstruction — a hold-up at the pelvis

One of the commonest causes of childhood hydronephrosis, at 1 in 1,000 to 1 in 1,500 births.8 Ureteric hypoplasia produces an abnormal smooth-muscle arrangement and an aperistaltic segment, so drainage fails functionally rather than being mechanically blocked.8

Usually found on second-trimester antenatal ultrasonography. Where it declares itself later in childhood, it does so as periodic abdominal or groin pain, vomiting, recurrent pyelonephritis and fever.8

Grading reflux

The five-grade classification in universal use comes from the International Reflux Study Committee and grades on how high the urine goes and how dilated the system is: grade 1, into a non-dilated ureter only; grade 2, up to the renal pelvis but without dilatation; grade 3, mild dilatation of ureter and pyelocalyceal system; grade 4, a tortuous moderately dilated ureter with blunted fornices but preserved papillary impressions; grade 5, severe dilatation with loss of both fornices and papillary impressions.7

Most grade 1 and 2 reflux resolves without intervention, as does about half of grade 3 and a smaller share of grades 4 and 5.3 Management turns on grade, whether there has been a febrile urinary tract infection, age and sex, and any coexisting bladder or bowel dysfunction — a relationship still being characterised.22 Antibiotic prophylaxis is used to prevent infection and renal damage while awaiting resolution, and surgery is reserved for recurrent infection despite prophylaxis, high-grade reflux, established renal damage, or a low likelihood of spontaneous resolution. (management, review consensus)

Assessing an obstructed pelvis

Diuretic renography and the split-function decision
The tracerTechnetium-99m mercaptoacetyltriglycine is the usual agent — secreted by the proximal tubules and filtered by the glomeruli, with its half-life correlating to split function.8
Below 40%The kidney is regarded as significantly damaged. Over 18 months of age with differential function under 40%, pyeloplasty is often recommended to prevent further loss — resecting the obstructed segment, replacing it with normal-calibre ureter and reattaching to the pelvis, open, laparoscopically or robot-assisted.8
Above 40%Over 18 months of age, scans are commonly repeated at 3, 6 and 12 months.8
Under 18 monthsObstruction may be transient and settle spontaneously over a few months.8

Posterior urethral valve — a blocked outlet

The commonest cause of lower urinary tract obstruction in neonates, at an estimated 1 in 5,000 to 1 in 8,000 births in the United States.9 An obstructing membranous flap or fold sits in the lumen of the posterior urethra in male infants, and its consequences run from urinary retention and chronic kidney disease through to pulmonary hypoplasia caused in utero by low amniotic fluid.9

✓ Findings that support the diagnosis

  • Bilateral hydronephrosis
  • Dilated prostatic urethra
  • Distended, thick-walled bladder — wall over 3 mm — emptying poorly across 30 minutes9
  • Serial antenatal scans tracking amniotic fluid and looking for dysplasia; fetal urinary electrolytes and β2-microglobulin can be measured to assess fetal renal function3

× Don’t over-read the keyhole sign

  • A dilated proximal urethra above a thick-walled distended bladder was long treated as diagnostic
  • More recent work questions how reliably it predicts a valve10
  • Postnatal presentation is non-specific — lethargy, poor feeding, delayed voiding, a palpable bladder, or urosepsis at the severe end9

Postnatally: correct electrolytes, manage respiratory distress or urosepsis, and catheterise for retention, usually with urology. Investigation can include renal and bladder ultrasonography, voiding cystourethrography and renal scintigraphy.9 Outcome follows the severity of obstruction and what it did in utero — in one series of 75 children with posterior urethral valves, 21% had reached end-stage renal failure by the end of a mean 64-month follow-up. Renal volume below the third centile, more than three febrile urinary tract infections, a reduced eGFR at one year, raised renal echogenicity and abnormal corticomedullary differentiation were all prognostic.11

Protect what is left

Many of these infants develop chronic kidney disease and bladder dysfunction and need long-term joint urology and nephrology follow-up. Avoid nephrotoxic drugs wherever you can — non-steroidal anti-inflammatories and aminoglycosides are the two that come up most.39

03 When the parenchyma is abnormal

Renal agenesis

Unilateral agenesis occurs in around 1 in 2,000 infants12 and may accompany the VACTERL association, a single umbilical artery, or contralateral reflux. An autosomal dominant inheritance pattern with several implicated gene mutations has been described, alongside maternal diabetes and certain drugs in pregnancy as possible causes.13

Bilateral agenesis is estimated at 1 in 8,500 infants and is typically incompatible with life.13 Both arise from failure of interaction between ureteric bud and metanephric mesenchyme.

Unilateral cases keep long-term function through a normal contralateral kidney but need annual review, because compensatory hypertrophy carries later risk of hypertension and proteinuria.1214 Reflux is common enough that voiding cystourethrography is a reasonable second-line investigation where ultrasonography suggests high-grade reflux or infections occur; in female infants, image the pelvis for müllerian duct anomalies.14

Renal dysplasia

Renal parenchyma is replaced, partly or wholly, by cartilaginous tissue or disorganised epithelial structures.4 It is the commonest cause of chronic kidney disease and renal failure in neonates.15

Several genes are implicated but the mechanisms remain poorly understood. It turns up frequently with obstructive uropathy and in the VACTERL and CHARGE associations, branchio-oto-renal syndrome, Jeune syndrome, and trisomies 13, 18 and 21.4

Function varies widely. Bilateral disease may show itself in the first days and often progresses through childhood and adolescence, with concentration and acidification defects along the way. There is no specific treatment; management is regular monitoring of blood pressure and kidney function.4

Multicystic dysplastic kidney

A severe form of dysplasia leaving a non-functioning kidney: normal architecture is absent, replaced by multiple large cysts often likened to a bunch of grapes.4 Seen in 1 in 1,000 to 1 in 4,300 live births, predominantly in males and on the left.16 Failure of the ureteric bud to merge and branch properly into the metanephros is one proposed mechanism.4

Most are unilateral, and around half come with extrarenal anomalies; bilateral disease is usually fatal. (review consensus) Most involute partially or completely over time,17 so management is conservative — serial ultrasonography to confirm involution and compensatory growth on the other side, with surgery reserved for a kidney that grows too large.

In unilateral disease, hypertension and malignancy do not appear to occur more often than in the general population.18

When kidney function fails before birth

The oligohydramnios (Potter) sequence follows severe fetal kidney dysfunction — bilateral dysplasia, bilateral obstruction, or autosomal recessive polycystic kidney disease — producing oligohydramnios and then compression of the fetus against the uterine wall.4

Look for a small compressed chest wall, clubfoot, hip dislocation and arthrogryposis, with posteriorly low-set ears, wide-set eyes, a beaked nose, depressed nasal bridge and receding chin.4

Respiratory failure from pulmonary hypoplasia — not the renal failure itself — is usually what these infants present with and what determines the first hours.4

04 When the kidney is in the wrong place, or doubled

Ectopic kidney

Normal development has the kidney ascend, rotate 90 degrees, and finish with medial rotation toward the hilum inside the first eight weeks.21 When that goes wrong the kidney sits abnormally, most often as a pelvic kidney, in roughly 1 in 1,000 individuals.3 In crossed ectopia one kidney crosses the midline and usually comes to lie below the contralateral kidney.

It may appear on routine antenatal scanning or be found postnatally as a palpable pelvic mass. Associations include reflux, contralateral dysplasia, cryptorchidism and hypospadias in males, and agenesis of the uterus and vagina or a unicornuate uterus in females. Work-up covers other anomalies, serial creatinine, voiding cystourethrography, and a technetium-99m dimercaptosuccinic acid scan for function.21

Horseshoe kidney

Around 1 in 500 infants, with a male predominance.19 The kidneys fuse at their inferior lobes and sit lower than usual; the isthmus is mostly renal parenchyma with a minority of fibrous tissue, and further ascent is typically prevented by the inferior mesenteric artery at L3.3

HNF1B has been associated with horseshoe kidney, though no specific aetiology is established;4 Edwards and Turner syndromes are recognised associations.19 Most infants are asymptomatic and it is found incidentally on ultrasonography or CT. Reflux is commoner than in the general population, so voiding cystourethrography has a role, and there is a higher incidence of nephrolithiasis plus increased risk of transitional cell carcinoma and Wilms tumour.19

Duplication of the collecting system is the commonest congenital kidney abnormality, with a female predominance; in about 8% of affected fetuses, ultrasonography shows abnormal urinary tract findings after 28 weeks’ gestation.320 Duplication is often incomplete, and its clinical weight comes from the company it keeps — reflux and ureteroceles, both of which raise infection risk.20 Confirmation can use intravenous urography, ultrasonography or CT, and management runs from observation to surgery depending on which segment is involved and how well it works.3

05 The newborn examination

Blood pressure and volume status first. Hypertension turns up with polycystic kidney disease, acute kidney injury, thrombosis or obstructive uropathy; hypotension with sepsis, haemorrhage or volume depletion. Oedema points to hydrops, acute kidney injury or congenital nephrotic syndrome; ascites to congenital nephrotic syndrome, obstruction or volume overload.4

Then the abdomen, where the single most useful statistic is this: two-thirds of neonatal abdominal masses are genitourinary in origin, and the commonest cause of a renal abdominal mass is hydronephrosis. Absent or lax abdominal musculature suggests Eagle-Barrett (prune belly) syndrome; a distended bladder suggests lower tract obstruction or a spinal cord lesion.4

External findings that should send you to the kidneys

  • Limb deformities; atypical external ears
  • Isolated microcephaly without known cause; hemihypertrophy; aniridia
  • Imperforate anus; cryptorchidism; abnormal external genitalia
  • Cloacal or bladder exstrophy; persistent urachus4

06 Investigations, and when to do them

Reading the numbers in a newborn
Serum creatinineImmediately after birth it reflects the pregnant person’s creatinine, not the baby’s. In term infants it falls from 0.6–1 mg/dL (53.04–88.40 µmol/L) to a mean of 0.4 mg/dL (35.36 µmol/L) across the first two weeks. In preterm infants the fall is slower and the nadir may take one to two months. A level that stays up, or climbs, means impaired function.4
UrinalysisFreshly voided urine is preferred; catheter sampling is best where culture is needed. Cloudiness may mean crystals or infection. Specific gravity is normally very low in neonates (under 1.004) but rises with high-molecular-weight solutes such as glucose or contrast agents.4
UltrasonographyFirst-line, and indicated for an abnormal antenatal scan, abdominal mass, acute kidney injury, hypertension, haematuria, congenital malformation, or a syndrome carrying urinary tract risk. Add Doppler of renal vessels and aorta where renovascular hypertension, thrombosis or acute kidney injury is suspected.4
Voiding cystourethrographyConsider for significant hydronephrosis, hydroureter or documented urinary tract infection; radiopaque contrast is instilled into the bladder through a catheter.4
Radioisotope scansGood for locating anomalous kidneys, identifying obstruction or scarring, and quantifying each kidney’s contribution — but hard to interpret in the first weeks because newborn glomerular filtration rate is relatively low.4

× Scanning too early

  • A non-urgent postnatal ultrasound performed before 48 hours can under-call hydronephrosis, because urine output has not yet established4
  • Reading a day-one creatinine as the baby’s own renal function4

✓ Getting the timing right

  • Non-urgent postnatal ultrasonography at 48 hours or later4
  • Severe antenatal hydronephrosis: rescan within 48 hours. Mild or moderate: after 48 hours8
  • Nephrology and urology early; add paediatric surgery, endocrinology and genetics where other anomalies are present4

07 What predicts the long term

Better antenatal diagnosis has driven more fetal intervention. That has reduced mortality, but it has also produced more surviving children living with renal dysfunction — which is why multidisciplinary planning now has to begin soon after birth rather than at a first outpatient appointment.252627 The early postnatal goals are surgical establishment of adequate urine flow, respiratory support where pulmonary hypoplasia is in play, and support of metabolic and electrolyte function, all aimed at holding off dialysis.23

In a birth cohort of 42 infants with severe congenital anomalies followed to a mean of around six years, management centred on preventing infection and preserving residual function — nutritional support with a typically whey-based formula individualised for electrolyte and nutritional balance, early introduction of growth hormone, and strict management of associated mineral bone disorder. Nadir serum creatinine predicted progression to chronic kidney disease with high sensitivity and specificity, and cystatin C predicted progression to end-stage renal disease. Survival tracked the severity of kidney disease.23

Over a longer horizon, a 2009 study of 312 patients preselected for anomalies of kidney number or size found 58 requiring dialysis by the age of 30 — a yearly incidence of 0.023 across 2,474 combined patient risk years. A solitary kidney, or renal hypodysplasia alongside posterior urethral valves, carried significantly higher risk.24

Fetal urine biochemistry is also used prognostically where fetal ultrasonography shows kidneys free of cortical cysts and hyperechogenicity — osmolality, sodium, chloride, calcium and β2-microglobulin each carry a favourable threshold. The values are set out in full by Poudel and colleagues and are best read there rather than quoted piecemeal.3

The point of all of it

Every strand converges on one aim: preserve kidney function, delay dialysis as long as possible, and reach pre-emptive transplantation rather than rescue.23 Preventing urinary tract infection and protecting residual nephron mass are not background housekeeping in this population — they are the treatment.

References

Each statement above is attributed to its primary source. Compiled with reference to Fong J, De Beritto T. Congenital anomalies of the kidneys and urinary tract. NeoReviews. 2024, and its cited literature. Items marked review consensus reflect described practice rather than trial evidence.

  1. Hays T, Thompson MV, Bateman DA, et al. The prevalence and clinical significance of congenital anomalies of the kidney and urinary tract in preterm infants. JAMA Netw Open. 2022;5(9):e2231626.
  2. Capone VP, Morello W, Taroni F, Montini G. Genetics of congenital anomalies of the kidney and urinary tract: the current state of play. Int J Mol Sci. 2017;18(4):796.
  3. Poudel A, Afshan S, Dixit M. Congenital anomalies of the kidney and urinary tract. NeoReviews. 2016;17(1):e18–e27.
  4. Vogt BA, Springel T. The kidney and urinary tract of the neonate. In: Martin RJ, Fanaroff AA, Walsh MC, eds. Fanaroff and Martin’s Neonatal-Perinatal Medicine: Diseases of the Fetus and Infant. Philadelphia, PA: Elsevier; 2020.
  5. Sargent MA. What is the normal prevalence of vesicoureteral reflux? Pediatr Radiol. 2000;30(9):587–593.
  6. Banker H, Aeddula NR. Vesicoureteral reflux. In: StatPearls. Treasure Island, FL: StatPearls Publishing; 2023. ncbi.nlm.nih.gov/books/NBK563262
  7. Medical versus surgical treatment of primary vesicoureteral reflux: report of the International Reflux Study Committee. Pediatrics. 1981;67(3):392–400.
  8. Al Aaraj MS, Badreldin AM. Ureteropelvic junction obstruction. In: StatPearls. Treasure Island, FL: StatPearls Publishing; 2023. ncbi.nlm.nih.gov/books/NBK560740
  9. Bingham G, Rentea RM. Posterior urethral valve. In: StatPearls. Treasure Island, FL: StatPearls Publishing; 2023. ncbi.nlm.nih.gov/books/NBK560881
  10. Bernardes LS, Aksnes G, Saada J, et al. Keyhole sign: how specific is it for the diagnosis of posterior urethral valves? Ultrasound Obstet Gynecol. 2009;34(4):419–423.
  11. Pohl M, Mentzel HJ, Vogt S, Walther M, Rönnefarth G, John U. Risk factors for renal insufficiency in children with urethral valves. Pediatr Nephrol. 2012;27(3):443–450.
  12. Cleveland Clinic. Renal agenesis. my.clevelandclinic.org
  13. Orphanet. Renal agenesis. orpha.net
  14. Groen In ‘t Woud S, Westland R, Feitz WFJ, et al. Clinical management of children with a congenital solitary functioning kidney: overview and recommendations. Eur Urol Open Sci. 2021;25:11–20.
  15. Phua YL, Ho J. Renal dysplasia in the neonate. Curr Opin Pediatr. 2016;28(2):209–215.
  16. National Institute of Diabetes and Digestive and Kidney Diseases. Multicystic dysplastic kidney. niddk.nih.gov
  17. Alamir A, Al Rasheed SA, Al Qahtani AT, et al. The outcome of multicystic dysplastic kidney disease patients at King Abdulaziz Medical City in Riyadh. Cureus. 2023;15(4):e37994.
  18. Chang A, Sivananthan D, Nataraja RM, Johnstone L, Webb N, Lopez PJ. Evidence-based treatment of multicystic dysplastic kidney: a systematic review. J Pediatr Urol. 2018;14(6):510–519.
  19. Kirkpatrick JJ, Leslie SW. Horseshoe kidney. In: StatPearls. Treasure Island, FL: StatPearls Publishing; 2023. ncbi.nlm.nih.gov/books/NBK431105
  20. Visuri S, Jahnukainen T, Taskinen S. Prenatal complicated duplex collecting system and ureterocele — important risk factors for urinary tract infection. J Pediatr Surg. 2018;53(4):813–817.
  21. Rosenblum ND. Kidney development. In: Gilbert SJ, Weiner DE, eds. National Kidney Foundation Primer on Kidney Diseases. 6th ed. Philadelphia, PA: WB Saunders; 2014:19–25.
  22. Lee H, Lee YS, Im YJ, Han SW. Vesicoureteral reflux and bladder dysfunction. Transl Androl Urol. 2012;1(3):153–159.
  23. Katsoufis CP, DeFreitas MJ, Infante JC, et al. Risk assessment of severe congenital anomalies of the kidney and urinary tract (CAKUT): a birth cohort. Front Pediatr. 2019;7:182.
  24. Sanna-Cherchi S, Ravani P, Corbani V, et al. Renal outcome in patients with congenital anomalies of the kidney and urinary tract. Kidney Int. 2009;76(5):528–533.
  25. Zurowska AM, Fischbach M, Watson AR, Edefonti A, Stefanidis CJ; European Paediatric Dialysis Working Group. Clinical practice recommendations for the care of infants with stage 5 chronic kidney disease (CKD5). Pediatr Nephrol. 2013;28(9):1739–1748.
  26. Kidney Disease: Improving Global Outcomes (KDIGO) CKD-MBD Update Work Group. KDIGO 2017 clinical practice guideline update for the diagnosis, evaluation, prevention, and treatment of chronic kidney disease–mineral and bone disorder (CKD-MBD). Kidney Int Suppl (2011). 2017;7(1):1–59.
  27. KDOQI Work Group. KDOQI clinical practice guideline for nutrition in children with CKD: 2008 update. Executive summary. Am J Kidney Dis. 2009;53(3 Suppl 2):S11–S104.

Tiny Taught · Neonatal & Paediatric Education

Educational content for qualified healthcare professionals, compiled independently from the published literature cited above. Not affiliated with, endorsed by, or produced under licence from any journal, professional body or certifying board. Not a continuing medical education activity.

Thresholds, doses and timings are given for orientation only; items marked as consensus reflect described practice rather than trial evidence. Always follow your local guidelines and seek specialist nephrology and urology input for individual infants.

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