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Endoscopic diagnosis of biliary disease is challenging due to difficulties in access, visualization, and sampling. Recent advances in endoscopic technology, ancillary diagnostic methods, and our understanding of autoimmune pancreatitis (AIP) and IgG4-related cholangitis (IRC) have led to improvements in the endoscopic diagnosis of pancreaticobiliary disease.Single-operator cholangioscopy overcomes several of the limitations of mother–baby cholangioscopy enhancing the diagnostic accuracy in indeterminate pancreaticobiliary disease. Probe-based confocal laser endomicroscopy has been recently shown to provide a significantly higher accuracy for the diagnosis of malignant biliary strictures than achieved by endoscopic retrograde cholangiopancreatogram and standard tissue acquisition, and has the potential to develop into a useful adjunct method of cholangioscopy. Fluorescence in-situ hybridization increases the sensitivity of routine brush cytology without compromising specificity in patients with indeterminate biliary strictures. The diagnosis of AIP/IRC remains challenging. The recently published international consensus criteria for AIP have included data on the potential diagnostic utility of endoscopic retrograde pancreatogram and endoscopic ampullary biopsies.Recent technical advances as well as ancillary diagnostic methods have improved the diagnostic accuracy of conventional endoscopic techniques. Future refinement of endoscopic methods may further improve diagnostic approaches to biliary disease.