The introduction of endoscopic retrograde cholangiopancreatography with endoscopic sphincterotomy (ES) has changed the treatment of choledocholithiasis. An increasing number of young patients are requiring ES, and this raises concern regarding any potential long-term complications arising from irreversibly altering the anatomy of the sphincter of Oddi. In particular, concern has been raised regarding the risk of late cholangiocarcioma. A review was performed evaluating the relationship between ES for benign disease and the subsequent development of late complications, including biliary tract malignancy, the formation of primary duct stones, and recurring cholangitis. A systematic review of articles published between 1970 and 2013 was undertaken. Current evidence shows that ES is a safe and effective treatment for common bile duct stones. The long-term risk of subsequent cholangiocarcinoma has not been convincingly proven although in many of these studies the follow-up period was inadequate. There does appear to be an associated increased incidence of cholangiocarcinomas following sphincterotomy although this is not proven to be causative. If there is an increased risk of cholangiocarcinoma following ES, it is likely to be small in western populations. However, until longer follow-up studies are published, it may be prudent to avoid ES in the very young.