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The authors present two cases of congenital choledochal cysts treated by cyst excision with Roux-en-Y hepaticojejunostomy, followed by good postoperative results. One of the patients has been treated by early excisional procedure, while the other has initially undergone an enteric drainage by cystoduodenostomy, followed by complications, which required reoperations after 18 months. We have evaluated the peculiarities of both cases, the present data revealed by literature regarding biliary carcinogenesis related to congenital choledochal cysts, their classification according to pancreatobiliary malunion, as well as the treatment of choice in choledochal cysts, meaning excisional procedure with Roux-en-Y hepaticojejunostomy to prevent the risk of postoperatory complications which might appear after plain enteric drainage of the cyst.