Probe-based confocal laser endomicroscopy is an endoscopic technique that enables in vivo histological evaluation using fluorescent pigment. The ability to diagnostically differentiate between benign and malignant biliary disease using the “CholangioFlexTM”, a dedicated biliary device, has been reported. However, the Miami and Paris classifications, used as diagnostic criteria, mainly evaluate findings in the submucosa, and visualizing the epithelium as the main site of lesions remains difficult. To address this problem, we verified the imaging findings and diagnostic ability of three types of probes: CholangioFlexTM, GastroFlexTM, and AlveoFlexTM. With GastroFlexTM, the clear mucosal epithelium was observed, and differential diagnoses as benign/malignant could be made based on epithelial findings. GastroFlexTM may be a good first-choice probe for probe-based confocal laser endomicroscopy of biliary diseases, and a new diagnostic classification based on bile duct epithelial findings may provide useful criteria independent of the Miami or Paris classifications.