Objective To investigate the efficacy of endoscopic papillary balloon dilation (EPBD) and endoscopic sphincterotomy (EST) in the treatment of non-dilated extrahepatic biliary stones. Methods The clinical data of 317 patients with non-dilated extrahepatic biliary stones who were admitted to the Taiyuan Iron and Steel Corporation Hospital from January 1999 to April 2008 were retrospectively analyzed. Of all patients, 119 received EPBD treatment, and the remaining 198 received EST treatment. Sixty-two patients treated by EPBD (EPBD group) and 62 by EST (EST group) were selected to conduct the matched-pair analysis. In the EPBD group, a cylindrical balloon was inserted under the guidance of a guidewire after the conclusive diagnosis by endoscopic retrograde cholangiopancreatography. After the dilation, stones were extracted by a stone basket or a balloon, and then conventional endoscopic nasobiliary drainage was carried out. In the EST group, stones were extracted by a stone basket or a balloon under the monitor of the digital subtraction radiography after incision of the duodenal papilla. The efficacy of the two methods was compared using the chi-square test. Results The stonefree rate in one session was 92% (57/62) in the EPBD group and 94% (58/62) in the EST group, with no significant difference between the two groups ( χ 2 = 0.222, P > 0.05 ). The number of patients who were complicated with hyperamylasemia and pancreatitis was slightly greater, and the number of patients who were complicated with duodenal perforation was smaller in the EPBD group than those in the EST group, while there was no significant difference between the two groups ( χ 2 = 0. 286, 1. 000, 2.000, P > 0.05 ). The numbers of patients who were complicated with duodenal papilla bleeding or biliary infection in the EPBD group were significantly smaller thanthose in the EST group ( χ 2 = 4. 000, 7. 000, P < 0.05 ). All patients were followed up for 24 months. The recurrence rate of bile duct stone and the incidence of biliary infection in the EPBD group were significantly lower than those in the EST group at the end of 6, 12 and 24 months (χ2 =4. 000, 5. 000, 6.000; 6.000, 8.000,11. 000, P < 0.05 ). Conclusions Combined application of EPBD and ENBD has the advantages of minor trauma and quick recovery of patients. It can preserve the function of duodenal papilla, so it is the first choice for treating non-dilated extrahepatic biliary stones.