Objective The safety and prognosis of complete stone removal for the treatment of choledocholithiasis in older patients are unknown. This multicenter retrospective study assessed the outcomes of complete stone removal in elderly patients (! 90 years) with respect to the prognosis. Methods We divided patients who underwent endoscopic cholangiopancreatography for choledocholithiasis into two groups: complete stone removal or incomplete stone removal with plastic stent insertion. The patient characteristics, adverse events, number of endoscopic cholangiopancreatographies, overall survival rates, and disease-specific cumulative death were compared between the groups. Patients Two hundred and twenty-three participants ! 90 years old were included in the study, including 48 (22%) men and 175 (78%) women. The median age was 92 (range, 90-104) years old. There were 160 (72%) and 63 (28%) patients in the complete and incomplete groups, respectively. Results: The age, performance status, comorbidities, severe complication rates, and stone diameter were comparable between the groups. The proportion of patients with at least 5 stones was significantly higher in the incomplete group than in the complete group (complete group: 8.1% [13/160] and incomplete group: 21% [13/63], p<0.01). The overall survival rate was significantly higher in the complete group (p<0.01), while the disease-specific cumulative death rate was higher in the incomplete group (p<0.01). Conclusion Complete stone removal for choledocholithiasis may contribute to a better prognosis in elderly patients ! 90 years old.