Congenital Gastrointestinal 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 embryonic development of the gut 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.

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.

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

  • The mnemonic 'VACTERL'[1] describes a condition of associated multiple abnormalities, some within and some outside the gut. It is diagnosed if there are at least 3 of the 6 defects.
    • V ertebral defects include single or multiple hemivertebrae, scoliosis or deformities of ribs.
    • A norectal malformations including imperforate anus and cloacal deformities.
    • C ardiovascular 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.
    • T racheo-oesophageal defect of (o)e sophageal atresia with or without tracheo-oesophageal fistula (TOF).
    • R enal anomalies including renal agenesis as with Potter's syndrome, bilateral renal agenesis or dysplasia, horseshoe kidney, polycystic kidneys, urethral atresia and ureteral malformations.
    • L imb deformities including radial dysplasia, absent radius, radial deformities, syndactyly, polydactyly, lower-limb tibial deformities.
  • A complex syndrome known by the mnemonic 'CHARGE'. Diagnosis requires 4 of 7 possible features, including at least 1 major feature.
    • C oloboma 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.
    • H eart 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.
    • A tresia 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.
    • R etardation 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.
    • G enital hypoplasia occurs in 70% of boys and 30% of girls. Micropenis, cryptorchidism and microlabia are described.
    • E ar 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 associated with situs inversus and gastrointestinal malformations. For example, giant hiatal hernias are associated with situs inversus totalis and Kartagener's syndrome. This presents with a history of chronic severe gastro-oesophageal reflux disease with uncontrolled regurgitation.[2]
  • 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.

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  • About 30% of such cases are part of syndromes with other abnormalities.
  • It is one of the most common congenital abnormalities with a worldwide incidence as high as 1 in 700. 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.
  • Oesophageal atresia occurs between 1 in 3,500 and 1 in 5,000 births. If a sibling has had the condition, that incidence is 1 in 50.
  • It is 6 times as common in twins as in singletons. 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 1 fistula and fistula without atresia. Feeding can lead to aspiration and early surgical repair is essential for survival.
  • 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.
  • Congenital diaphragmatic hernia permits the stomach to ascend in part into the thoracic cavity. This may occur with deficiency of the diaphragm.
  • As well as causing trouble with feeding, if it is gross, the stomach will impinge on the structures in the chest and cause embarrassment to breathing and circulation.
  • Early surgical repair is required.
  • Hypertrophic pyloric stenosis is sometimes called congenital pyloric stenosis (a misnomer as it is not present at birth but develops soon after).
  • 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 (ratio about 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 2 and 8 weeks after birth, although it can present as early as the first week and as late as 5 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. After a feed, the enlarged olive-like pyloric 'tumour' may be palpable.
  • Ultrasound is now used more often to assist diagnosis of the condition.
  • Ramstedt's operation involves longitudinal incision of the pyloric sphincter down to the mucosa. An inadequate depth will be ineffective but too far will perforate the gut.
  • 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.
  • Presentation is with persistent vomiting, often bilious, within hours of birth, although sometimes it my take a couple of days to develop. Lower lesions take longer to develop symptoms.
  • X-ray will show fewer air levels than expected. 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.[3]
  • 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. There may be other features of intestinal obstruction.
  • Barium enema may show malposition of the colon.
  • Ultrasound and CT may also be of value.
  • Management is surgical correction.
  • Meckel's diverticulum is a vestigial remnant of the vitellointestinal duct on the ante-mesenteric border of the ileum.
  • 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 does not always 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 vitellointestinal bands, also cause volvulus. It can also cause intussusception or present like an acute appendicitis.
  • If it causes problems it can be surgically resected.
  • Hirschsprung's disease is caused by failure of development of the neural ganglia in the myenteric and submucosal plexus of the rectum.
  • The incidence is around 1 in 5,000 births with boys affected 4 times as often as girls.
  • 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.
  • Minor abnormalities of the anus or rectum occur in about 1 birth in every 500 but major abnormalities are around 1 in 5,000.
  • Associated abnormalities of the small intestine, oesophagus, genitourinary system, cardiovascular system and sacral area may also occur.
  • 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 is not usually required.
  • Preoperative resuscitation is required. The nature of surgery depends upon the precise lesion and other possible complications. Meticulous management gets good results.[4][5] The importance of accurate diagnosis before surgery is illustrated by a review of management of patients with newborn cloacas.[6]

Further reading & references

  • Reid JR; Hypertrophic Pyloric Stenosis, eMedicine, Aug 2009
  • Tegay D et al; CHARGE Syndrome, eMedicine, Nov 2009
  • Lewis N et al; Duodenal Atresia and Stenosis - Surgical Perspective, eMedicine, Mar 2010
  • Levitt M et al; Imperforate Anus, Surgical Treatment, eMedicine, Feb 2010
  • Rosen NG et al; Imperforate Anus (Paediatric perspective), eMedicine, Jan 2010
  1. 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.
  2. Hoang CD, Bakman YG, Ikramuddin S, et al; Situs inversus totalis: giant hiatal hernia repair by laparoscopic Collis gastroplasty and Nissen fundoplication. Surg Endosc. 2004 Feb;18(2):345-9.
  3. 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.
  4. Levitt MA, Pena A; Anorectal malformations. Orphanet J Rare Dis. 2007 Jul 26;2:33.
  5. Levitt MA, Pena A; Outcomes from the correction of anorectal malformations. Curr Opin Pediatr. 2005 Jun;17(3):394-401.
  6. Levitt MA, Pena A; Pitfalls in the management of newborn cloacas. Pediatr Surg Int. 2005 Apr;21(4):264-9. Epub 2005 Feb 22.

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 Richard Draper
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Document ID:
1993 (v21)
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