Enteric duplication cysts (EDCs) are uncommon congenital anomalies, which can occur anywhere along the gastrointestinal tract and vary greatly in presentation, size, location and symptoms. Ectopic gastric mucosa is reported to be found in 20-30% of these duplications. (99m)Tc-pertechnetate scintigraphy is a useful modality for preoperative localization of the ectopic functioning gastric mucosa in the EDCs. We report a case where (99m)Tc-pertechnetate scintigraphy was useful in detecting synchronous thoracic and abdominal duplication cysts with functioning gastric mucosa thus having an impact on the patient management.