Expanded polytetrafluoroethylene grafts are widely used for middle hepatic vein reconstruction during living-donor liver transplant because they have comparable patency to autologous or cryopreserved vessels. Mechanical complications like gastric or duodenal penetration by expanded polytetrafluoroethylene grafts have been infrequently reported. We recently experienced a case of duodenal penetration by the expanded polytetrafluoroethylene graft. The patient was a 57-year-old man who had undergone a living-donor liver transplant for cryptogenic liver cirrhosis. At an annual follow-up computed tomography scan performed 3 years after transplant, the expanded polytetrafluoroethylene graft appeared to have penetrated into the first to the second portion of the duodenum, and abnormal air shadow and partial thrombus were identified within the expanded polytetrafluoroethylene graft. The patient underwent exploratory laparotomy, the expanded polytetrafluoroethylene graft was removed, and the perforated duodenum was repaired. Pyloric exclusion with gastrojejunostomy and feeding jejunostomy was additionally performed because of a wide defect in the duodenum. Adjacent organ injuries such as duodenal or gastric penetration by the expanded polytetrafluoroethylene graft after living-donor liver transplant is rare but not uncommon. Because the use of expanded polytetrafluoroethylene grafts is essential when an adequate vessel allograft is unavailable, we can consider transposition of the omental flap between the expanded polytetrafluoroethylene graft and the stomach or duodenum to reduce this unexpected complication.