We present a case of oesophageal atresia with distal tracheo-oesophageal fistula and duodenal atresia, which later on was detected to have cystic variant of biliary atresia. He underwent primacy repair of oesophageal atresia with ligation of distal tracheo-oesophageal fistula and duodenoduodenostomy. He later developed features of obstructive jaundice, and on investigation was diagnosed to have cystic variant of biliary atresia which was initially confused with iatrogenic biliary obstruction. Exploration and operative cholangiogram with biopsy confirmed cystic variant of biliary atresia and underwent successful Kasai procedure. Our case effectively demonstrates a rare triology of foregut atresia without an apparent genetic association. It highlights stepwise systematic management of foregut atresias in this patient and demonstration of cystic variant of biliary atresia. Even though these are rarely seen, still the clinician should be aware of such a possibility and should adopt a multimodality approach to diagnose and an aggressive approach to manage the condition.