Choledochal cysts are malformations of the biliary ductal system, which rarely occur in infancy. In neonates and infants, choledochal cysts are congenital, may be associated with distal biliary atresia and typically presents with cholestatic jaundice and acholic stools characteristic of biliary obstruction. In older children and adults, it may be acquired in association with an anomalous pancreaticobiliary union and presents with any combination of intermittent jaundice, abdominal pain, and a palpable abdominal mass. Early detection of choledochal cysts is important in the prevention of the fatal complications of biliary obstruction. Here, we present two cases of congenital choledochal cyst in which the patients were 9 weeks old and 7 weeks old respectively. Both of them presented with jaundice, acholic stools, and hepatomegaly. Combined use of sonography, computed tomography and hepatobiliary scintigraphy demonstrated the presence of choledochal cysts. Thereafter, they underwent surgical excision of the cysts with Roux-en-Y reconstruction of the biliary tree; the results were successful.