Definitive preoperative diagnosis of esophageal and gastric duplication is difficult. We report a case of these extremely rare diseases which were successfully treated by operation. Operative ultrasonography was attempted and revealed that both esophageal and gastric duplications were separated from the mucosa, indicating the possibility of excision by means of enucleation. These cystic lesions showed different features in terms of ultrasound echogenicity (sonolucent versus echogenic lumen). Operative ultrasound examination may be a valuable assistance during surgery of gastrointestinal tumors, in particular submucosal tumors, for accurate intraoperative diagnosis and appropriate operative management.