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Congenital gastrointestinal malformations

Medical Professionals

Professional Reference articles are designed for health professionals to use. They are written by UK doctors and based on research evidence, UK and European Guidelines. You may find one of our health articles more useful.

The embryonic development of the gastrointestinal (GI) tract is complex and it is perhaps unsurprising that abnormalities of development occur. They may be complex and multiple with more than one part of the gut affected or other systems involved. This article will focus on structural defects rather than defects of gut function involving, for example, enzyme deficiency.

Congenital anomalies of the GI tract commonly present in the neonatal period or early infancy. Some abnormalities may be suspected before birth. For example, defects that impair swallowing will produce polyhydramnios. Many abnormalities are not at first apparent although they may be associated with multiple other defects. Rarely, they can present as de novo cases in adolescence.1 Some of them can have life-threatening consequences if diagnosis is delayed. Therefore, the prognosis is largely dependent on early diagnosis and management including surgical correction.

Although the outcome of newborns with surgical congenital diseases (eg, diaphragmatic hernia, oesophageal atresia, omphalocoele, gastroschisis) has improved rapidly with recent advances in perinatal intensive care and surgery, infant survivors often require intensive treatment after birth, have prolonged hospitalisations and, after discharge, may have long-term sequelae including gastro-intestinal comorbidities, particularly gastro-oesophageal reflux.2

Low socio-economic status, poor prenatal diagnosis, prematurity, postnatal diagnostic delay, obsolete medical equipment and the lack of neonatal intensive care units are major factors for high mortality in neonates with gastrointestinal tract malformations in developing countries.3

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Risk factors

The complexity of embryonic development is reflected in the varied range of syndromes and abnormalities associated with GI malformations. This is illustrated by many associated conditions and syndromes. For example:4

  • The mnemonic 'VACTERL' describes a condition of associated multiple abnormalities, some within and some outside the gut.5 Initially named as the VATER association, the condition is usually sporadic and the incidence is estimated between 1 in 10,000 to 40,000 births.6 It is diagnosed if there are at least three of the six defects.

    • Vertebral defects include single or multiple hemivertebrae, scoliosis or deformities of ribs.

    • Anorectal malformations including imperforate anus and cloacal deformities.

    • Cardiovascular defects, especially ventricular septal defect (the most common), Fallot's tetralogy, patent ductus arteriosus, atrial septal defects, aortic coarctation, right-sided aortic arch, single umbilical artery, and others.

    • Tracheo-oesophageal defect of (o)Esophageal atresia with or without tracheo-oesophageal fistula (TOF).

    • Renal anomalies including renal agenesis as with Potter's syndrome, bilateral renal agenesis or dysplasia, horseshoe kidney, polycystic kidneys, urethral atresia and ureteral malformations.

    • Limb deformities including radial dysplasia, absent radius, radial deformities, syndactyly, polydactyly, lower-limb tibial deformities.

  • A complex syndrome known by the mnemonic 'CHARGE'. Diagnosis requires four of seven possible features, including at least one major feature. The syndrome can have a broad phenotypic spectrum with some clinical features being more common than others. Genetic testing for CHD7 mutation (most common genetic defect) should therefore be considered in neonates with specific combination of several clinical symptoms.7

    • Coloboma of the eye affects 80%. It is often bilateral. The eye is small and there is nystagmus in severe cases but, if the coloboma does not involve the fovea, vision is unaffected unless retinal detachment occurs.

    • Heart anomalies occur in 70%. Various types of congenital cardiovascular defects are described but ventricular septal defect and atrial septal defect are the most common. Fallot's tetralogy and patent ductus arteriosus are also quite common.

    • Atresia means posterior choanal atresia. It occurs in 50%. Half have bilateral involvement which usually presents in the newborn period with respiratory distress. Mouth breathing cannot be established and life is threatened. Polyhydramnios in pregnancy is often present. When bilateral and especially if associated with cyanotic heart disease, few children live beyond a year.

    • Retardation is both developmental retardation and physical. In 70% there is intrauterine growth restriction as well as failure to grow and thrive. Mental retardation occurs in 70% with possible microcephaly and cerebral atrophy.

    • Genital hypoplasia occurs in 70% of boys and 30% of girls. Micropenis, cryptorchidism and microlabia are described.

    • Ear abnormalities and deafness affect 90%. The external ear is usually abnormal, often being small and low-set. Deafness if often of mixed type.

  • Kartagener's syndrome is an autosomal recessive condition associated with situs inversus and GI malformations. A significant proportion of patients with situs inversus have congenital GI malformations such as duodenal atresia, biliary atresia, gastroschisis with malrotation or TOF.8

  • The Pentalogy of Cantrell is a rare syndrome comprising defects of the diaphragm, abdominal wall, heart and sternum. Specifically, the syndrome includes omphalocele, diaphragmatic hernia (anterior), sternal cleft and ectopia cordis.

Cleft lip and palate9

  • About 30% of such cases are part of syndromes with other abnormalities.

  • Approximately 70% of cases occur as isolated entities with no other apparent cognitive or structural abnormalities (isolated, non-syndromic cleft lip and palate).

  • It is one of the most common congenital abnormalities but the incidence seems to have fallen. An epidemiological study reviewed data from 2002 to 2006 in 30 countries and estimated a worldwide incidence of about 0.8 per 1,000, which is much lower than older studies.10 The incidence of cleft palate alone is about 1 in 2,000.

  • Taking certain anticonvulsants, benzodiazepines and steroids in pregnancy increases the risk.

  • The appearance may inhibit maternal bonding. There may be difficulties in feeding and with speech.

  • Generally, the results of surgical treatment are extremely good.

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Oesophageal atresia4

  • Oesophageal atresia has an estimated incidence of 1 in 3,000 births. The recurrence risk in subsequent pregnancies of oesophageal atresia that is not part of a syndrome is less than 1%.

  • It is two to three times more common in twins than in singletons.11 It is more common in the trisomy disorders of Down's syndrome, Patau's syndrome and Edwards' syndrome.

  • About half have other congenital abnormalities too, usually of urogenital, cardiovascular or colorectal systems. Hence, there would seem to be some genetic component involved but its contribution is unclear.

  • Around 85% have a distal tracheo-oesophageal fistula. Around 10% have no fistula and the remainder is a mixture of proximal fistula, more than one fistula and fistula without atresia. Feeding can lead to aspiration and early surgical repair is essential for survival.

See separate Oesophageal Atresia article.

Exomphalos and gastroschisis

  • Exomphalos and gastroschisis occur in about 1 birth in 3,000.

  • There is a deficiency of the abdominal wall and contents can herniate into this space.

  • Prune belly syndrome is a rare condition in which about 97% are boys. There is deficiency of the abdominal wall and cryptorchidism, hydronephrosis and possibly pulmonary hypoplasia but the gut is usually intact.

See separate Exomphalos and Gastroschisis article.

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Congenital diaphragmatic hernia

  • Congenital diaphragmatic hernia results from failure of diaphragm to fuse during fetal development allowing abdominal organs to migrate into the chest.

  • Presence of abdominal viscera in the chest interferes with lung development and can result in pulmonary hypoplasia and pulmonary hypertension in severe cases.

  • Diagnosis is often made antenatally and most cases are symptomatic at birth, requiring ventilatory support and aggressive treatment of pulmonary hypertension.

  • Milder cases can present later in life, sometimes even in adulthood.

  • Surgical repair which involves replacing the abdominal contents into the abdominal cavity and repairing the diaphragmatic defect should be done after full stabilisation of the patient.12

See separate Congenital Diaphragmatic Hernia article.

Hypertrophic pyloric stenosis

  • Hypertrophic pyloric stenosis is caused by diffuse hyperplasia of the smooth muscle of the stomach antrum and pylorus

  • It was described by Hirschsprung in 1888 and, in 1907, Ramstedt described the operation which still bears his name.

  • It is strikingly more common in boys (reported ratios 2:1 to 5:1) and more common in first-born children. It is significantly more common in the white population than in other racial groups.

  • The incidence is 2 to 4 per 1,000.

  • The symptoms are due to failure of gastric emptying so that feeding is followed by projectile vomiting in which the vomit may be propelled for a considerable distance.

  • Vomiting tends to start between two and eight weeks after birth, although it can present as early as the first week and as late as five months. There is failure to gain weight and the projectile vomiting is characteristic. Projectile vomit has no bile in it. It is dramatic and not to be confused with exaggerated descriptions of non-projectile vomiting. The vomit is propelled some distance and can, for example, cross a room.

  • Early diagnosis and treatment reduces morbidity and particularly the effects of electrolyte disturbance (hypochloraemic metabolic alkalosis and dehydration).

  • Test feeding is used in diagnosis but is not always positive. After a feed, the enlarged olive-like pyloric 'tumour' may be palpable.

  • Ultrasound is highly sensitive and specific and increasingly used to confirm the diagnosis.13

  • Ramstedt's operation involves longitudinal incision of the pyloric sphincter down to the mucosa. It has very low risk of complications and an excellent success rate.

See separate Infantile Hypertrophic Pyloric Stenosis article.

Intestinal atresia, stenosis and webs

  • These can occur at any level but the most common place for atresia, after the oesophagus, is the duodenum. The incidence of duodenal atresia is between 1 in 10,000 and 1 in 30,000 births. Around a third to a half have other abnormalities too. About 30% have Down's syndrome. About 30% have cardiovascular defects.

  • Antenatal detection by ultrasound is often possible and polyhydramnios may be a presenting feature.

  • Presentation is with persistent vomiting, often bilious, within hours of birth, although sometimes it may take a couple of days to develop. Lower lesions take longer to develop symptoms.

  • X-ray will show fewer air levels than expected and may reveal the classical double bubble sign of duodenal atresia. Colonic atresia may also occur. It takes longer to develop and air levels are more normal.

  • A barium enema may show a small colon, suggestive of a distal small-bowel obstruction. It is also capable of demonstrating other causes of lower obstruction, such as Hirschsprung's disease or a meconium plug. The enema may also enter the small bowel and help demonstrate the level of a distal obstruction.

  • Surgical correction is required but resuscitation and correction of dehydration must precede surgery. The order or priorities may depend upon other abnormalities.

  • Combined oesophageal and duodenal atresia makes the situation much more complicated.14

See separate Oesophageal Strictures, Webs and Rings article.

Volvulus and midgut rotation

  • Volvulus is a complete twisting of a loop of intestine around its mesenteric attachment and can happen anywhere in the GI tract.

  • Midgut volvulus refers to the twisting of entire midgut along the axis of superior mesenteric artery and is the most common type of volvulus.

  • This may present in the first week of life but usually in the first year.

  • Symptoms are bilious vomiting and intestinal obstruction, although in older children it may be simply recurrent abdominal pain and colic.

  • Plain abdominal X-ray shows the double bubble of duodenal obstruction in cases of volvulus. There may be other features of intestinal obstruction such as multiple dilated bowel loops and fluid levels

  • Upper GI contrast studies are the most useful investigation although selected patients may benefit from a barium enema.

  • Barium enema may show malposition of the colon.

  • Ultrasound and CT may also be of value.

  • Management is surgical correction.

See separate Volvulus and Midgut Malrotations article.

Meckel's diverticulum

  • Meckel's diverticulum is a vestigial remnant of the vitello-intestinal duct and is the most common malformation of the GI tract.

  • It is often remembered as occurring in 2% of the population, 2 feet from the caecum and being on average 2 inches in length.

  • It usually does not cause problems and may be an incidental finding at operation or autopsy.

  • Around half may contain heterotopic tissue, usually gastric mucosa.

  • It can produce massive rectal bleeding in a child. It can, with associated vitello-intestinal bands, also cause volvulus. It can also cause intussusception or present like an acute appendicitis.

  • If it causes problems it can be surgically resected.

See separate Meckel's Diverticulum article.

Hirschsprung's disease

  • Hirschsprung's disease is caused by failure of development of the neural ganglia in the myenteric and submucosal plexus of the rectum.

  • A study from the North of England reported an incidence of 1.65 per 10,000 live births with a male to female ratio of 2:1.15

  • Delayed passage of meconium is a crucial feature, as nearly half of all infants with Hirschsprung's disease do not pass meconium within 36 hours, and nearly half of infants with delayed first passage of meconium have Hirschsprung's disease.

  • The affected segment of bowel is of normal calibre whilst the bowel proximal to it is dilated.

  • A defunctioning colostomy may be required to permit return to normal of the dilated bowel and then the aganglionic segment must be resected.

  • It is associated with a number of other conditions but especially Down's syndrome.

See separate Hirschsprung's Disease article.

Imperforate anus16

  • Minor abnormalities of the anus or rectum occur in about 1 birth in every 500 but major abnormalities are around 1 in 5,000.

  • Despite the relatively common occurrence of imperforate anus, prenatal diagnosis is rarely reported.

  • Cases of isolated imperforate anus exist, but most commonly this condition is found as one among a wide spectrum of other anomalies, particularly VATER or VACTERL (see above), but other associations, syndromes and sequences have also been frequently reported to include anorectal anomalies.

  • Failure to pass meconium in the first 24 hours of life should lead to examination of the rectum. Milder lesions may cause constipation later on.

  • If there is an adequate amount of gas in the bowel, a plain X-ray will usually suffice for diagnosis. CT or ultrasound may also be required.

  • Pre-operative resuscitation is required. The nature of surgery depends upon the precise lesion and other possible complications. Meticulous management results in good results.17 18

Further reading and references

  1. Vaos G, Misiakos EP; Congenital anomalies of the gastrointestinal tract diagnosed in adulthood--diagnosis and management. J Gastrointest Surg. 2010 May;14(5):916-25. doi: 10.1007/s11605-009-1124-z. Epub 2009 Dec 22.
  2. Marseglia L, Manti S, D'Angelo G, et al; Gastroesophageal reflux and congenital gastrointestinal malformations. World J Gastroenterol. 2015 Jul 28;21(28):8508-15. doi: 10.3748/wjg.v21.i28.8508.
  3. Camara S, Fall M, Mbaye PA, et al; Congenital malformations of the gastrointestinal tract in neonates at aristide le dantec university hospital in Dakar: Concerning 126 cases. Afr J Paediatr Surg. 2022 Jul-Sep;19(3):133-136. doi: 10.4103/ajps.AJPS_37_21.
  4. Ludwig K, De Bartolo D, Salerno A, et al; Congenital anomalies of the tubular gastrointestinal tract. Pathologica. 2022 Feb;114(1):40-54. doi: 10.32074/1591-951X-553.
  5. Shaw-Smith C; Oesophageal atresia, tracheo-oesophageal fistula, and the VACTERL association: review of genetics and epidemiology. J Med Genet. 2006 Jul;43(7):545-54. Epub 2005 Nov 18.
  6. Solomon BD; VACTERL/VATER Association. Orphanet J Rare Dis. 2011 Aug 16;6:56. doi: 10.1186/1750-1172-6-56.
  7. Husu E, Hove HD, Farholt S, et al; Phenotype in 18 Danish subjects with genetically verified CHARGE syndrome. Clin Genet. 2013 Feb;83(2):125-34. doi: 10.1111/j.1399-0004.2012.01884.x. Epub 2012 Apr 30.
  8. Lee SE, Kim HY, Jung SE, et al; Situs anomalies and gastrointestinal abnormalities. J Pediatr Surg. 2006 Jul;41(7):1237-42.
  9. Dixon MJ, Marazita ML, Beaty TH, et al; Cleft lip and palate: understanding genetic and environmental influences. Nat Rev Genet. 2011 Mar;12(3):167-78. doi: 10.1038/nrg2933.
  10. Tanaka SA, Mahabir RC, Jupiter DC, et al; Updating the epidemiology of cleft lip with or without cleft palate. Plast Reconstr Surg. 2012 Mar;129(3):511e-518e. doi: 10.1097/PRS.0b013e3182402dd1.
  11. Spitz L; Oesophageal atresia. Orphanet J Rare Dis. 2007 May 11;2:24.
  12. Bosenberg AT, Brown RA; Management of congenital diaphragmatic hernia. Curr Opin Anaesthesiol. 2008 Jun;21(3):323-31.
  13. Niedzielski J, Kobielski A, Sokal J, et al; Accuracy of sonographic criteria in the decision for surgical treatment in infantile hypertrophic pyloric stenosis. Arch Med Sci. 2011 Jun;7(3):508-11. doi: 10.5114/aoms.2011.23419. Epub 2011 Jul 11.
  14. Dave S, Shi EC; The management of combined oesophageal and duodenal atresia. Pediatr Surg Int. 2004 Sep;20(9):689-91. Epub 2004 Sep 11.
  15. Best KE, Glinianaia SV, Bythell M, et al; Hirschsprung's disease in the North of England: prevalence, associated anomalies, and survival. Birth Defects Res A Clin Mol Teratol. 2012 Jun;94(6):477-80. doi: 10.1002/bdra.23016. Epub 2012 Apr 18.
  16. Brantberg A, Blaas HG, Haugen SE, et al; Imperforate anus: A relatively common anomaly rarely diagnosed prenatally. Ultrasound Obstet Gynecol. 2006 Dec;28(7):904-10. doi: 10.1002/uog.3862.
  17. Levitt MA, Pena A; Anorectal malformations. Orphanet J Rare Dis. 2007 Jul 26;2:33.
  18. Levitt MA, Pena A; Outcomes from the correction of anorectal malformations. Curr Opin Pediatr. 2005 Jun;17(3):394-401.

Article History

The information on this page is written and peer reviewed by qualified clinicians.

  • Next review due: 19 Aug 2028
  • 21 Aug 2023 | Latest version

    Last updated by

    Dr Colin Tidy, MRCGP

    Peer reviewed by

    Dr Pippa Vincent, MRCGP
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