Congenital duodenal atresia is usually associated with various congenital anomalies. The embryological events in the development of the biliary tract and duodenum are linked. Although an association between duodenal atresia and biliary anomalies is predictable, it is rarely observed. We describe the case of a 27 year-old woman, operated on for duodenal atresia in her childhood, who presented cholangiolitis. Morphologic investigation allowed the diagnosis of choledochal cyst with an intracystic stone developed in the pancreatic head. A pancreatico-duodenectomy was performed because of the importance and the location of dilatation and stone with biliary obstruction. To our knowledge, the association between a congenital duodenal atresia and a choledochal cyst revealed at adult age had never been described in the literature.