Alimentary tract duplication cysts are rarely diagnosed in utero. We report two fetal patients that presented with intrathoracic alimentary tract duplication cysts, mediastinal shift and hydrops. In one fetus, the cyst continued into the fetal abdomen and pelvis through a left diaphragmatic hernia. Despite successful ultrasound-guided needle aspirations in both fetuses, there was rapid reaccumulation of the fluid and recurrence of the mediastinal shift, prompting the placement of a thoracoamniotic shunt. In one fetus, there was rapid resolution of the mediastinal shift with the disappearance of the hydrops within 2 weeks. The second fetus suffered an intrauterine demise 2 days after the shunt placement. Postnatal resection in the surviving infant revealed a large cyst consistent with an intrathoracic duplication of the stomach. The autopsy of the second fetus revealed an intrathoracic duplication cyst of the stomach and proximal small intestine.