OBJECTIVE Endoscopic papillary balloon dilatation (EPBD), which allows preservation of papillary functions, is used as the first-line therapy in our hospital for common bile duct (CBD) stones to reduce biliary complications. In the present study, we investigated causal factors for CBD stones and compared long-term prognosis between EPBD and endoscopic sphincterotomy (EST). METHODS A total of 453 EPBD and 233 EST cases treated between April 1996 and May 2007 were examined. They were categorized into four groups: group 1, gallbladder (GB) with stones was resected after CBD stones were extracted (cholecystectomy for GB with stones); group 2, GB with stones was not resected after CBD stones were extracted (no cholecystectomy for GB with stones); group 3, only CBD stones were extracted while the GB without stones was not resected (GB without stones); and group 4, CBD stones with a history of cholecystectomy (absence of GB). Then, postoperative recurrence of CBD stones was compared. To examine changes in papillary functions by EPBD, Oddi's sphincter pressure was measured before and after EPBD. RESULTS Recurrence was observed in 31 EPBD and 40 EST cases. When recurrence rates by EPBD/EST were compared among the four treatment groups, they were lower with EPBD than with EST in all groups. Oddi's sphincter functions were preserved by 70% after EPBD. CONCLUSIONS Low-pressure EPBD in combination with isosorbide dinitrate enabled preservation of papillary functions by 70%, which would improve a long-term prognosis.