Overview of Digestive Tract Birth Defects

ByJaime Belkind-Gerson, MD, MSc, University of Colorado
Reviewed/Revised Modified Aug 2025
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A birth defect can occur in any of the organs that make up the digestive tract: the esophagus, stomach, small intestine, large intestine, rectum, and anus.

  • 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 abdominal pain, abdominal swelling, and vomiting.

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

  • Surgery usually is required.

Birth defects along the digestive tract can include the following:

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 along the digestive tract, including in the esophagus, intestines, rectum, or anus. Sometimes a segment of the digestive tract does not form or develop normally or forms and then is destroyed by a problem that occurs in the womb before birth. 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 not develop, as is the case with Hirschsprung disease.

Symptoms of Digestive Tract Birth Defects

Symptoms depend on what the birth defect is and where it is located.

Infants may have abdominal pain, abdominal swelling, vomiting, or a combination. Problems with feeding can occur, and infants may not gain weight normally.

Some infants develop a yellowish discoloration of the skin and whites of the eyes called jaundice.

Diagnosis of Digestive Tract Birth Defects

  • Imaging tests (x-ray and ultrasound)

Imaging tests are usually required to diagnose a digestive tract birth defect.

In many cases, defects can be detected before birth during routine prenatal ultrasound.

After birth, some defects are diagnosed with x-rays of the chest or abdomen. Ultrasound 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, such as genetic testing, may be done depending on the other test results and symptoms.

Treatment of Digestive Tract Birth Defects

  • Surgery

Most digestive tract defects require surgery. Typically, blockages are surgically opened. Holes in the walls of the abdominal cavity are surgically repaired.

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