We present a rare case of congenital intrathoracic stomach due to short esophagus in a preterm infant. Antenatal ultrasound during the second trimester showed a tubular cystic structure in the posterior mediastinum. The diagnosis of congenital hiatal hernia was initially made. After birth, the diagnosis was confirmed to be intrathoracic stomach associated with a congenitally short esophagus by upper gastrointestinal contrast study and laparotomy. Features that suggest intrathoracic stomach secondary to congenital short esophagus over the relatively more common congenital hiatal hernia include early identification of the intrathoracic stomach during the second trimester and the consistent absence of an abdominal stomach bubble on antenatal ultrasound. The infant’s condition could not be surgically repaired due to the extremely malformed and short esophagus and she subsequently died. This is in sharp contrast to the more surgically amenable and non-life-threatening congenital hiatal hernia. Early recognition of intrathoracic stomach associated with congenital short esophagus is important as it is associated with difficult management and significant postnatal complications. Fetal magnetic resonance imaging may be useful in this situation. The prognosis is cautiously guarded, and the parents should be appropriately counseled.

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