BACKGROUND Pyloric duplication is an extremely rare gastrointestinal tract malformation in neonates. This is the first case report of pyloric duplication in our country (Lithuania). METHODS We report the case of a 2-day-old Lithuanian girl who suffered from pyloric duplication mimicking an alternative common bile duct cyst or other intra-abdominal organs cysts. A laparotomy was performed and the cystic formation of the pyloric area was successfully resected. The postoperative course was uneventful. CONCLUSIONS There are only a few reports describing abdominal masses caused by pyloric duplication mimicking common bile duct cyst or other intra-abdominal organs cysts. Therefore thorough clinical and instrumental examination is needed to determine the most accurate diagnosis that allows one to choose the right treatment.