The association of foregut atresias and bile duct anomalies is reportedly rare. We encountered five referrals within 2 years where the secondary diagnosis was missed at operation. Four patients initially presented on antenatal scans as a foregut atresia whereas the fifth presented at nine years with abdominal pain due to a choledochal cyst. The biliary anomalies (cholecysto-hepatic duct, liver cyst and choledochal cysts) in the first four presented as postoperative jaundice during infancy whereas the fifth patient developed subacute intestinal obstruction due to congenital duodenal stenosis at fifteen years. In the patients with duodenal atresia neither did the preoperative X ray reveal any distal bowel gas nor did the subsequent intraoperative cholangiograms reveal bifid common bile duct or pancreato-biliary malunion. Atresias were corrected by primary repair (duodenoduodenostomy for congenital duodenal obstruction in four patients and disconnection/ligation of tracheo-oesophageal fistula with oesophageal anastomosis in one patient). The biliary anomalies were corrected by excision of the abnormal bile ducts (choledochal cyst/liver cyst/cholecystectomy) with Roux en Y hepaticojejunostomy. All patients are asymptomatic and liver function and biliary dilatation has normalised. The association of foregut atresias and bile duct anomalies is not as rare as previously reported. Antenatal ultrasound suggesting either a foregut or a biliary anomaly should alert one to the association. Full radiological and/or imaging investigation may be indicated prior to corrective surgery of the primary anomaly.