This study assessed factors influencing the complete removal and recurrence of bile duct stones in patients with surgically altered anatomy (SAA) undergoing double-balloon endoscopy-assisted endoscopic retrograde cholangiography (DBERC). A retrospective analysis of 289 patients with SAA treated for biliary stones with DBERC at Jichi Medical University Hospital (January 2007 to December 2022) was conducted. Evaluation of factors impacting complete stone removal was performed in 257 patients with successful bile duct cannulation. Logistic and Cox proportional hazards regression models were used to compute the odds ratios (ORs) and hazard ratios (HRs) at 95% confidence intervals (CIs). Of 257 patients, 139 (54.0%) and 209 (81.3%) achieved initial and complete removal, respectively. Recurrence occurred in 55 (21.4%) patients. Factors associated with initial complete stone removal included cholangitis (P < 0.01, OR 0.48, 95% CI 0.27-0.83), number of stones (P < 0.01, OR 0.31, 95% CI 0.18-0.54), and largest stone diameter (P < 0.01, OR 0.37, 95% CI 0.20-0.67). The size of the largest stone was associated with complete removal (P = 0.01, OR 0.24, 95% CI 0.13-0.76). Recurrence was associated with cholangitis (P = 0.046, HR 0.54, 95% CI 0.29-0.99), congenital biliary dilatation (P = 0.01, HR 2.65, 95% CI 1.21-5.80), and number of stones (P = 0.02, HR 1.96, 95% CI 1.12-3.41). Successful complete bile stone removal in patients with SAA depends on the stone diameter and number. Stone recurrence is influenced by the number of stones and history of congenital biliary dilatation.