Congenital web formations are extremely rare anomalies of the extrahepatic biliary tree. The age at presentation and the clinical symptomatology of these anomalies depend on the grade of the biliary obstruction. We report a case of a common bile duct septum in association with cholelithiasis in a 30-year-old woman. The diagnosis was made on preoperative magnetic resonance cholangiopancreatography (MRCP) and confirmed with intraoperative cholangiography. Because all known causes of acquired web formation were excluded, a congenital origin of the web was assumed. The patient was treated with a hepaticoduodenostomy above the level of the septum. The embryological aspects of this rare anomaly are described.