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Purpose To prospectively compare the navigator-echo triggering technique (navigator technique) and the conventional respiratory triggering technique using bellows (bellows technique) for free-breathing three-dimensional (3D) magnetic resonance cholangiopancreatography (MRCP) under clinical conditions. Materials and methods Forty patients referred for evaluation of biliary or pancreatic diseases underwent 3D MRCP examination using both navigator and bellows techniques. Two independent radiologists visually evaluated the image quality of 12 segments of the pancreaticobiliary tree in a blinded manner. In addition, the clarity of the lesion was compared between the two techniques in a side-by-side manner. Result MRCP images were successfully acquired using both techniques in all patients. No significant difference in acquisition time was found between the two techniques. The image quality was significantly better using the navigator technique than using the bellows technique for the following seven segments: the head, body, and tail of the pancreatic duct; right hepatic duct; anterior and posterior segments of the right hepatic duct; and cystic duct. The other segments (common hepatic and bile duct, left hepatic duct, medial and lateral segments of left hepatic duct, gallbladder) showed no significant difference. The clarity of lesion depiction was significantly better using the navigator technique than using the bellows technique. Conclusion Respiratory-triggered 3D MRCP using the navigator technique was shown to be feasible in routine clinical practice. The navigator technique improved the image quality of free-breathing 3D MRCP compared with the bellows technique. The clarity of lesion visualization was also better using the navigator technique than using the bellows technique.