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Objectives: Although peroral cholangioscopy has improved the endoscopic treatment of difficult stones, the treatment of intrahepatic stones remains challenging. The incidence of cholangitis is high when peroral cholangioscopy is used to treat intrahepatic stones. This study aimed to investigate the efficacy and safety of endoscopic treatment with peroral cholangioscopy for intrahepatic and common bile duct stones. Methods: Patients aged ≥20 years, who underwent endoscopic treatment with peroral cholangioscopy for intrahepatic or common bile duct stones at Tottori University Hospital from January 2016 to December 2022, were retrospectively evaluated to determine the efficacy and safety of the treatment. Results: Overall, 70 patients were included in this study: 22 in the intrahepatic stone group and 48 in the common bile duct stone group. Stones were smaller (8 vs. 17.5 mm, p < 0.001) and more numerous (p = 0.016) in the intrahepatic stone group than in the common bile duct stone group. Although the common bile duct stone group exhibited a higher rate of complete stone clearance in the first session, no significant differences were observed in the final results. The intrahepatic stone group had a higher incidence of cholangitis (36% vs. 8%, p = 0.007); however, all cases were mild. Conclusions: Endoscopic treatment with peroral cholangioscopy for intrahepatic stones may be associated with a higher incidence of cholangitis than that for common bile duct stones. Since saline irrigation may contribute to the development of cholangitis, it is important to be aware of intraductal bile duct pressure when performing peroral cholangioscopy. [ABSTRACT FROM AUTHOR]