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Background/Aims There are few studies assessed the efficacy and mortality of endoscopic retrograde cholangiopancreatography (ERCP) for the removal of common bile duct (CBD) stones in the elderly aged ≥90 years. We aimed to assess the safety and efficacy of endoscopic removal of CBD stones in nonagenarians. Methods We retrospectively reviewed ERCP reports for CBD stone removal. The endoscopic and therapeutic outcomes were collected. The length of stay (LOS), the total number of adverse events, and mortality rate were compared between groups. Results A total of 125 nonagenarians were compared with 1,370 controls (65–89 years old individuals). The mean LOS for nonagenarians was significantly higher than in controls (13.6 days vs. 6.5 days). Completed intended treatment was similar in the nonagenarians and controls (89.8% and 89.5%, respectively). The overall complication rate did not differ between the groups. However, nonagenarians had a higher incidence of post-ERCP pneumonia (3.9%). None of the nonagenarians were readmitted to the hospital within 7 days. Four nonagenarians (3.2%) and 25 (1.8%) controls died within 30 days. Conclusions Advanced age alone did not affect the decision to perform the procedure. However, prompt diagnosis and treatment of post-ERCP pneumonia in nonagenarians could improve the outcomes and reduce mortality.