We assessed whether the presence of juxtapapillary duodenal diverticula (JPDD) risks biliary stone disease and recurrence. In total, 695 patients who underwent ERCP were divided into two groups: biliary stone disease (group I, n = 523) and non-stone biliary diseases (group II, n = 172). Additionally, for a control group (group III), 80 age-matched healthy subjects underwent side-view duodenoscopy. In group I, rates of post-ERCP pancreatitis, cannulation failure, and disease recurrence in two-year follow up were compared according to the presence of JPDD. In results, the incidence of JPDD in group I (42.4%) was significantly higher than in group II (16.3%) and III (18.8%). The frequencies of JPDD were increased with age in all groups, and reached statistical significance in group I. In group I, rates of post-ERCP pancreatitis were significantly higher in patients with JPDD (18.5%) compared to JPDD negative (12.6%). The cannulation failure rate was also higher in patients with JPDD (9.9%) compared to JPDD negative (5.3%). Recurrence rate was higher in patients with JPDD (25.3%) compared to JPDD negative (9.2%). In conclusion, JPDD develops with aging and risks biliary stone formation. JPDD also seems to be associated with post-ERCP pancreatitis, cannulation failure and biliary stone recurrence.