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To assess the short-term outcomes after endoscopic sphincterotomy (EST) plus endoscopic papillary balloon dilation (EPBD) versus EPBD alone and appropriate balloon dilation time in EPBD alone.A total of 413 patients with common bile duct stones (CBDSs) were included in the EST plus EPBD group and 84 were in the EPBD alone group. We retrospectively evaluated the safety and efficacy between EST plus EPBD and EPBD alone group. The patients in EPBD alone group were assigned to dilation time ≥5 minutes group (n=35) and time <5 minutes group (n=49). Further, we preliminarily discussed the influence of balloon dilation time on the procedure-related complications.Compared with EST plus EPBD, the patients in EPBD alone group were younger [56.6 (range: 18 to 95) vs. 65.1 (24 to 92) y; P=0.006], had smaller diameter of the largest stone [10.4 (range: 3 to 20) vs. 12.3 (5 to 30) mm; P<0.001] and were lesser frequently performed with jaundice [22 (26.2%) vs. 189 (45.8%); P=0.001]. The mean duration of postoperative hospital stay in EPBD alone group was significantly shorter than EST plus EPBD group [6.3 (range: 1 to 18) vs. 9.2 (1 to 44) d; P<0.001]. The patients in EPBD alone group had higher risk of post endoscopic retrograde cholangiopancreatography pancreatitis than EST plus EPBD group [11 (13.1%) vs. 22 (5.3%); P=0.009]. Patients in the dilation time <5 minutes group had higher risk to suffer from postoperative pancreatitis than the EST plus EPBD group [9 (18.4%) vs. 22 (5.3%); P=0.002], while patients in the dilation time ≥5 minutes group had less procedure-related hemorrhage than the EST plus EPBD group [0 vs. 36 (8.7%); P=0.047].Long balloon dilation time in EPBD alone is safe and effective in treating CBDSs.