Congenital malformations of the gastrointestinal tract

PDF download is not available for Arabic and Urdu languages at this time. Please use the browser print function instead

Read about various types of congenital malformations of the GI tract. These birth defects are rare, but potentially serious.

Key points

  • In rare cases, some babies are born with congenital malformations of the GI tract, which are unrelated to premature birth.
  • Conditions range from mild to severe and can occur anywhere from the esophagus to the anus.
  • More common malformations include: esophageal atresia and fistula; intestinal atresias; malrotation with volvulus; Hirschsprung's disease; anorectal malformations; and abdominal wall defects.

Sometimes babies are born with malformations somewhere along the gastrointestinal (GI) tract. These malformations are not caused by prematurity and are rare. They range from minor to serious and can occur anywhere from the esophagus to the anus. Many of these conditions can be surgically treated, with an excellent chance at normal development and function later on as the baby grows into childhood and beyond. Other malformations have outcomes that are not as good.

Esophageal atresia and fistula

Esophageal atresia and fistula are malformations in which the natural breathing tube, known as the trachea, and the feeding tube, called the esophagus, are improperly formed. Most often the upper esophagus lacks a connection to the stomach while the lower esophagus connects to the trachea through an abnormal passage called a fistula. Babies with these types of malformations are fed with total parenteral nutrition (TPN) or with a feeding tube directly into the stomach. During this time, the baby gains strength and the esophagus will continue to grow. After several weeks, the malformation is repaired with surgery. About 20% of babies with these types of malformations will also have other complications, such as heart disease.

Tracheoesophageal fistula and esophageal atresia Normal esophagus and trachea, and an illustration of tracheoesophageal fistula and esophageal atresia
Tracheoesophageal fistula is a small opening between the windpipe and the esophagus. It often occurs in combination with esophageal atresia, a condition in which the esophagus is not properly connected to the stomach. Babies born with these conditions are fed with a feeding tube directly into the stomach. After several weeks, the malformations are repaired with surgery.

Intestinal atresias

Intestinal atresias are malformations of the intestines in which a segment of bowel is very narrow or is disconnected from the rest of the GI tract. Most commonly, these occur in or near the duodenum, just below the stomach. Although atresias are rare, babies born with this condition are often small for their gestational age and some may also have Down syndrome. Depending on exactly where the malformation is, bile may be released into the GI tract with nowhere to go but up, appearing in the esophagus. As with esophageal atresia, the malformation is repaired with surgery, though the exact nature of the malformation may mean surgery will be performed sooner rather than later.

Intestinal atresia Normal stomach, duodenum and small intestine and an illustration of duodenal atresia with the site of atresia identified
Intestinal atresia is a malformation where part of the intestine is very narrow or disconnected from the rest of the gastrointestinal tract. Most often, this occurs at a spot just below the stomach called the duodenum. Intestinal atresia can be repaired with surgery.

Malrotation with volvulus

Until about the 10th week of pregnancy, a fetus’s GI tract develops, in part, in the umbilical cord. At this point, it returns to the abdomen and rotates 90 degrees to the right. The individual components of the GI tract, including the duodenum, which connects the stomach and the intestines, and the intestines themselves, rearrange themselves and begin to settle into a position that will then remain unchanged for the rest of a person’s life. At the end of this process, the GI tract is normally fixed; that is, it is contained and supported, and does not move.

Occasionally, this series of maneuvers and migrations is not performed properly and part of the GI tract, though still connected, ends up in the wrong place. This malrotation, as it is called, can also leave the GI tract unfixed. In some cases, this is not a problem; some people end up leading a normal life with an unfixed and rotated bowel. However, many babies have severe symptoms. Occasionally, as the GI tract settles itself into place, it loops around itself, reducing its blood supply or causing an obstruction. This is called volvulus. Malrotation with volvulus requires emergency surgery to correct the problem.

Malrotation with volvulus Simplified picture of normal stomach and small and large intestines, and an illustration of malrotation with volvulus
If the gastrointestinal tract does not develop properly, parts of it can end up in the wrong place. This is called malrotation. Sometimes the gastrointestinal tract ends up looping around itself to the extent that a blockage forms that could reduce the blood supply, and this is called volvulus. Malrotation with volvulus requires emergency surgery.

Hirschsprung’s disease

Hirschsprung’s disease is a condition in which nerve cells called ganglia have not formed on the inner wall of the bowel. This causes the bowel to contract and not relax, obstructing the lower intestine. Boys are about 10 times more likely to have the disease than girls. Again, surgery is used to correct the malformation. Surgeons will identify the bowel section without ganglia, cut it out, and reattach the two ends of healthy bowel. Sometimes a colostomy, or the surgical removal of some of the bowels, is necessary, and the surgeons will do the final repair at six to 12 months of age. Many babies who have undergone this procedure will develop and lead normal lives, since enough functioning bowel remains for digestion. However, a small number of babies with Hirschsprung’s disease also have an inflammation of the large intestine called colitis, which may complicate surgery and can be life threatening.

Anorectal malformations

Some babies are born with malformations of the anus, rectum, or both. There are several general types. They have varying degrees of severity and are treated with surgery. These malformations are often specific to boys and girls. The malformation can come in the form of an absence of an opening where the anus should be; a fistula, or small opening from the rectum to the urinary tract or to the vagina; and many variations from these general categories. Depending on the exact nature and severity of the malformation, babies may be left completely continent, with full control over their bowel movements; partially continent; or incontinent. In general, surgeons will close the fistula and, in the case of a missing anus, create an opening and gently pull though the bottom of the bowel, creating a new anus.

Abdominal wall defects

A defect in the abdominal wall may allow some of the digestive system to develop outside the baby’s body in the amniotic fluid of the womb. These rare abnormalities are usually very small and only a small portion of the intestines are exposed. Gastroschisis occurs on the abdominal wall. Omphalocele occurs on the umbilicus, or belly button. Each of these defects allows some of the digestive system to develop outside the body. They can be small or large, and involve one organ or several.

Sometimes, these conditions can be diagnosed before birth. Exposure to the amniotic fluid can cause damage to the intestines. For this reason, some hospitals may suggest a planned early caesarean section to limit the extent of intestinal exposure to amniotic fluid. There is still debate about whether this is the best course of action. The treatment is surgical reinsertion of the intestines into the body. Depending on the size and extent of the condition, there may be more than one surgery needed to accomplish this goal.

Though in general they are very rare, there are many other types of malformations not mentioned on this page.

More information

Last updated: October 31st 2009