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Overview of Congenital Gastrointestinal Anomalies


William J. Cochran

, MD, Geisinger Clinic

Last full review/revision Apr 2021| Content last modified Apr 2021
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Most congenital gastrointestinal (GI) anomalies result in some type of intestinal obstruction, frequently manifesting with feeding difficulties, distention, and emesis at birth or within 1 or 2 days. Some congenital GI malformations, such as malrotation, have a very good outcome, whereas others, such as congenital diaphragmatic hernia, have a poor outcome (mortality rate of 10 to 30%).

A common type of anomaly is atresia, in which a segment of the GI tract fails to form or develop normally, or it forms and then is destroyed by an intrauterine event (vascular disruption). The most common type is esophageal atresia, followed by atresia in the jejunoileal region and in the duodenum.

Immediate management includes bowel decompression (by continuous nasogastric suction to prevent emesis, which can lead to aspiration pneumonia or further abdominal distention with respiratory compromise) and referral to a center for neonatal surgery. Also vital are maintenance of body temperature, prevention of hypoglycemia with IV 10% dextrose and electrolytes, and prevention or treatment of acidosis and infections so that the infant is in optimal condition for surgery.

Because about one third of infants with a GI malformation have another congenital anomaly (up to 50% in those with congenital diaphragmatic hernia and up to 70% in those with omphalocele), they should be evaluated for malformations of other organ systems, especially of the central nervous system, heart, and kidneys.

High Alimentary Tract Obstruction

Esophageal, gastric, duodenal, and sometimes jejunal obstruction should be considered when excess amniotic fluid (polyhydramnios) is diagnosed, because such obstructions prevent the fetus from swallowing and absorbing amniotic fluid.

A nasogastric tube should be passed into the neonate’s stomach immediately after cardiovascular stability has been attained after delivery. Finding large amounts of fluid in the stomach, especially if bile-stained, supports the diagnosis of upper GI obstruction, whereas inability to pass the tube into the stomach suggests esophageal atresia (or nasal obstruction [eg, choanal atresia]).

Jejunoileal and Large-Bowel Obstruction

Obstruction of the jejunum and ileum can occur as the result of jejunoileal atresia, malrotation, or meconium ileus. Large-bowel obstruction is typically caused by meconium plug syndrome, or colonic or anal atresia.

In 75% of cases, no history of maternal polyhydramnios exists because much of the swallowed amniotic fluid can be absorbed from the intestine proximal to the obstruction. These disorders, other than malrotation, intestinal duplication, and Hirschsprung disease, typically manifest in the first few days of life with feeding problems, abdominal distention, and emesis that may be bilious or fecal. The neonate may pass a small amount of meconium initially but thereafter does not pass stools. Malrotation, intestinal duplication, and Hirschsprung disease can manifest in the first several days of life or years later.

General diagnostic approach and preoperative management include the following:

  • Giving nothing by mouth

  • Placing a nasogastric tube to prevent further bowel distention or possible aspiration of vomitus

  • Correcting fluid and electrolyte disturbances

  • Taking a plain abdominal x-ray

  • Doing a contrast enema to delineate the anatomy (the enema may also relieve obstruction in meconium plug syndrome or meconium ileus)

For Hirschsprung disease, a rectal biopsy is needed.

Defects in Abdominal Wall Closure

Several congenital defects involve the abdominal wall (eg, omphalocele, gastroschisis), allowing protrusion of the viscera through the defect.

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