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Background Heterotopic gastrointestinal cysts have gastrointestinal epithelium in the cyst wall and rarely occur in the oral cavity. Most are found in the neonatal period. However, heterotopic gastrointestinal cysts that are diagnosed as a congenital tongue cyst by routine ultrasonography are extremely rare. Case summary A 12-day-old female presented with swelling of the anterior tongue. The obstetrician had detected significant tongue swelling on fetal ultrasonography in the 35th gestational week. The female was born by cesarean delivery at gestational week 39. She soon became dyspneic, and the cyst was aspirated. After the aspiration, her breathing recovered and she started breastfeeding. The cyst was excised under general anesthesia on the 67th day. Histopathologic examination showed that that cyst wall consisted of a lining of columnar gastrointestinal-type epithelium and pseudostratified ciliated epithelium. The patient restarted breastfeeding 3 h after surgery. The postoperative course was uneventful. Conclusion Airway distress and feeding difficulty were successfully avoided by cyst aspiration, and surgical resection was performed with no perioperative complications.