It causes increased levels of amniotic fluid during pregnancy (polyhydramnios) and intestinal obstruction in newborn babies.

Newborns present with bilious or non-bilous vomiting (depending on where in the duodenum the obstruction is) within the first 24 to 48 hours after birth, typically after their first oral feeding.

Bilious or non-bilious vomiting, depending on the position of the atresia in relation to the Ampulla of Vater, commonly occurs within the first day of life.

[citation needed] Approximately 20–40 percent of all infants with duodenal atresia have Down syndrome and 50% have a congenital cardiac anomaly.

[6][7] The air is trapped in the stomach and proximal duodenum, which are separated by the pyloric sphincter, creating the appearance of two bubbles visible on x-ray.

[9] A limited upper gastrointestinal series using barium contrast can be used to differentiate between duodenal atresia and midgut volvulus.