Most congenital gastrointestinal (GI) anomalies present as intestinal obstruction with signs including feeding difficulties, abdominal distention, emesis, and an inability to pass gas and stool at birth or within 1 or 2 days of age. Some congenital GI malformations, such as malrotation, have a very good outcome, whereas others, such as congenital diaphragmatic hernia, have a poor outcome (including an overall mortality rate of approximately 25%) (1).
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, such as a 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 cause aspiration pneumonia) and to prevent further abdominal distention (which can exacerbate respiratory compromise). Early referral to a neonatal surgical center is critical. Also vital are maintenance of body temperature, prevention of hypoglycemia and intravascular volume depletion with dextrose and electrolyte-containing IV fluids, and prevention or treatment of acidosis and infections so the infant is in optimal condition for surgery.Immediate management includes bowel decompression by continuous nasogastric suction to prevent emesis (which can cause aspiration pneumonia) and to prevent further abdominal distention (which can exacerbate respiratory compromise). Early referral to a neonatal surgical center is critical. Also vital are maintenance of body temperature, prevention of hypoglycemia and intravascular volume depletion with dextrose and electrolyte-containing IV fluids, and prevention or treatment of acidosis and infections so the infant is in optimal condition for surgery.
Because many infants with a GI malformation may have another congenital anomaly (eg, approximately 20% in those with gastroschisis, 50% in those with congenital diaphragmatic hernia or anorectal malformation, 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 (2, 3, 4).
Esophageal, Gastric, and Duodenal Obstruction
Esophageal, gastric, duodenal, and sometimes jejunal obstruction should be considered when excess amniotic fluid (polyhydramnios) is seen on a prenatal ultrasound because such obstructions prevent the fetus from swallowing and absorbing amniotic fluid.
Once cardiovascular stability has been attained after delivery, a nasogastric tube should be passed into the neonate’s stomach. Large amounts of fluid in the stomach, especially if bile-stained, supports the diagnosis of upper GI obstruction. Inability to pass the tube into the stomach suggests esophageal atresia.
Once the neonate is stable, radiographic studies are performed for further evaluation.
Jejunoileal and Large-Bowel Obstruction
(See also Meconium Ileus and Meconium Plug Syndrome.)
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, colonic atresia, or anal atresia.
In many cases, there is no history of maternal polyhydramnios because much of the swallowed amniotic fluid can be absorbed from the intestine proximal to the obstruction. Disorders that result in bowel obstruction, other than malrotation, intestinal duplication, and Hirschsprung disease, typically resent in the first few days of life with feeding problems, abdominal distention, and emesis that may be bilious or fecaloid. The neonate may pass a small amount of meconium initially but thereafter does not pass stools. Malrotation, intestinal duplication, and Hirschsprung disease can present at a variety of ages, ranging from the first several days of life to years later. Hirschsprung disease may also present as a neonatal colonic perforation (5).
General diagnostic approach and preoperative management include the following:
No oral food or liquid intake
Nasogastric tube to prevent further bowel distention or possible aspiration of vomitus
Correction of fluid and electrolyte disturbances
Abdominal radiographs
In addition, a contrast enema may be helpful to delineate the anatomy and may also relieve the obstruction in neonates with meconium plug syndrome or meconium ileus. If Hirschsprung disease is suspected from the contrast enema, a confirmatory rectal biopsy is required.
Defects in Abdominal Wall Closure
Several congenital defects involve the abdominal wall (eg, omphalocele, gastroschisis), allowing protrusion of the viscera through the defect.
Diaphragmatic Hernia
Congenital diaphragmatic hernia results in a defect in the diaphragmatic wall. Abdominal contents, including intestines, stomach, and liver, may protrude through the defect into the thoracic cavity, resulting in pulmonary hypoplasia.
Meckel Diverticulum
A Meckel diverticulum is a congenital remnant of the umbilical cord and the intestine leading to a small sac or outpouching of the small intestine. It is present in < 1 to 3% of the general population (6). Most diverticula are asymptomatic, but in a small percentage of patients they may manifest as intestinal obstruction or as gastrointestinal bleeding.
References
1. Gupta VS, Harting MT, Lally PA, et al. Mortality in Congenital Diaphragmatic Hernia: A Multicenter Registry Study of Over 5000 Patients Over 25 Years. Ann Surg. 2023;277(3):520-527. doi:10.1097/SLA.0000000000005113
2. Stoll C, Alembik Y, Roth MP. Co-occurring non-omphalocele and non-gastroschisis anomalies among cases with congenital omphalocele and gastroschisis. Am J Med Genet A. 2021;185(7):1954-1971. doi:10.1002/ajmg.a.62112
3. Stoll C, Dott B, Alembik Y, Roth MP. Associated anomalies in cases with anorectal anomalies. Am J Med Genet A. 2018;176(12):2646-2660. doi:10.1002/ajmg.a.40530
4. Alexe PI, Torres AS, Ebanks AH, et al. Prematurity and Congenial Diaphragmatic Hernia: Revisiting Outcomes in a Contemporary Cohort. J. Pediatr. 2025;114545. doi:10.1016/j.jpeds.2025.114545
5. Komuro H, Urita Y, Hori T, et al. Perforation of the colon in neonates. J Pediatr Surg. 2005;40(12):1916-1919. doi:10.1016/j.jpedsurg.2005.08.006
6. Hansen CC, Søreide K. Systematic review of epidemiology, presentation, and management of Meckel's diverticulum in the 21st century. Medicine (Baltimore). 2018;97(35):e12154. doi:10.1097/MD.0000000000012154
