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Overview of Digestive Tract Birth Defects

By William J. Cochran, MD, Associate, Department of Pediatrics, GI, and Nutrition, Geisinger Clinic; Clinical Professor, Department of Pediatrics, Temple University School of Medicine

  • The digestive organs may be incompletely developed or abnormally positioned, causing blockages, or the muscles or nerves of the digestive tract may be defective.

  • Symptoms depend on the location of the defect but may include crampy abdominal pain, abdominal swelling, and vomiting.

  • The diagnosis usually is based on imaging tests and other tests.

  • Surgery usually is required.

A birth defect can occur anywhere along the length of the digestive tract—in the esophagus, stomach, small intestine, large intestine, rectum, or anus. Such birth defects include the following:

Biliary atresia is a birth defect involving the bile ducts. Although the bile ducts are located outside the digestive tract, they help with digestion and are thus mentioned here.

In many cases, an organ is not fully developed or is abnormally positioned, which often causes narrowing or blockage (obstruction). Blockages can be present almost anywhere in the digestive tract, including in the esophagus, intestines, rectum, or anus. The internal or external muscles surrounding the abdominal cavity may weaken or develop holes, as is the case with abdominal wall defects and diaphragmatic hernia. The nerves to the intestines may also fail to develop (as is the case with Hirschsprung disease).


Symptoms depend on what the birth defect is and where it is located. Infants may have crampy abdominal pain, abdominal swelling, and/or vomiting. Problems with feeding can occur and infants may fail to gain weight normally. Some infants develop a yellowish discoloration of the skin called jaundice.


  • Imaging tests (x-rays and ultrasonography)

Imaging tests are usually required to diagnose a digestive tract birth defect. Sometimes, defects are detected before birth during routine prenatal ultrasonography. After birth, some defects are diagnosed with x-rays of the chest or abdomen. Ultrasonography may also be done after birth to identify and locate defects.

Other testing may include blood tests and biopsies. During a biopsy, a piece of tissue is removed for examination under a microscope.

Other tests are done depending on the test results and symptoms.


  • Surgery

Most digestive tract defects require surgery. Typically, blockages are surgically opened. Weakenings or holes in the muscles surrounding the abdominal cavity are sewn shut.