Abnormalities in partitioning of the esophagus and trachea by the tracheoesophageal septum result in esophageal atresia with or without tracheoesophageal fistulas (TEF). These defects occur in approximately 1/3000 births, and 90% result in the upper portion of the esophagus ending in a blind pouch and the lower segment forming a fistula with the trachea. Isolated esophageal atresia and H-type TEF without esophageal atresia each account for 4% of these defects. Other variations each account for approximately 1% of these defects. These abnormalities are associated with other birth defects, including cardiac abnormalities, which occur in 33% of these cases. In this regard, tracheoesophageal fistulas are a component of the VACTERL association (Vertebral anomalies, anal atresia, cardiac defects, tracheoesophageal fistula, esophageal atresia, renal anomalies, and limb defects), a collection of defects of unknown causation, but occuring more frequently than predicted by chance alone.

A complication of some tracheoesophageal fistulas is polyhydramnios, since in some types of tracheoesophageal fistulas amniotic fluid does not pass to the stomach and intestines for absorption and subsequent transfer through the placenta to the mothers blood for disposal. Also, gastric contents and/or amniotic fluid may enter the trachea through a fistula, causing pneumonitis (inflammation of the lung tissue) and pneumonia (inflammation of the parenchyma of the lungs).