Introduction:Duodenal obstructions caused by congenital anatomic abnormalities are rare in adults. Several patients in whom the duodenal obstruction was caused by a congenital duodenal diaphragm have been described. The duodenal obstruction in the patient presented herein was caused by a transverse septum, which has not been previously reported. A transverse septum is usually observed in the vagina; those involving the digestive tract have been rarely observed.Case Presentation:We herein report a case involving a 69-year-old woman with a congenital duodenal transverse septum causing partial obstruction. She was admitted to our hospital with a 3-month history of epigastric pain and vomiting. Upper gastrointestinal endoscopy, iodinated water-soluble contrast imaging, and abdominal computed tomography revealed dilation of the stomach and a neoplasm in the descending part of the duodenum. The patient was suspected to have a tumor in the descending part of the duodenum. Exploratory laparotomy showed a banded duodenal transverse septum at the junction of the second part of the duodenum. The duodenal transverse septum was approximately 2mm thick and 1cm wide and divided the duodenal lumen into 2 parts. The duodenal papillae were completely normal and located under the duodenal transverse septum. Histopathological analysis of the transverse septum showed that it was similar to the organizational structure of the duodenal wall.Conclusion:The possibility of congenital disease should be considered in older patients with intestinal obstruction, even when imaging studies reveal a duodenal neoplasm.