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Objectives: To compare the image quality of three-dimensional breath-hold magnetic resonance cholangiopancreatography with deep learning-based compressed sensing reconstruction (3D DL-CS-MRCP) to those of 3D breath-hold MRCP with compressed sensing (3D CS-MRCP), 3D breath-hold MRCP with gradient and spin–echo (3D GRASE-MRCP) and conventional 2D single-shot breath-hold MRCP (2D MRCP). Methods: In total, 102 consecutive patients who underwent MRCP at 3.0 T, including 2D MRCP, 3D GRASE-MRCP, 3D CS-MRCP, and 3D DL-CS-MRCP, were prospectively included. Two radiologists independently analyzed the overall image quality, background suppression, artifacts, and visualization of pancreaticobiliary ducts using a five-point scale. The signal-to-noise ratio (SNR) of the common bile duct (CBD), contrast-to-noise ratio (CNR) of the CBD and liver, and contrast ratio between the periductal tissue and CBD were measured. The Friedman test was performed to compare the four protocols. Results: 3D DL-CS-MRCP resulted in improved SNR and CNR values compared with those in the other three protocols, and better contrast ratio compared with that in 3D CS-MRCP and 3D GRASE-MRCP (all, p < 0.05). Qualitative image analysis showed that 3D DL-CS-MRCP had better performance for second-level intrahepatic ducts and distal main pancreatic ducts compared with 3D CS-MRCP (all, p < 0.05). Compared with 2D MRCP, 3D DL-CS-MRCP demonstrated better performance for the second-order left intrahepatic duct but was inferior in assessing the main pancreatic duct (all, p < 0.05). Moreover, the image quality was significantly higher in 3D DL-CS-MRCP than in 3D GRASE-MRCP. Conclusion: 3D DL-CS-MRCP has superior performance compared with that of 3D CS-MRCP or 3D GRASE-MRCP. Deep learning reconstruction also provides a comparable image quality but with inferior main pancreatic duct compared with that revealed by 2D MRCP. Key Points: • 3D breath-hold MRCP with deep learning reconstruction (3D DL-CS-MRCP) demonstrated improved image quality compared with that of 3D MRCP with compressed sensing or GRASE. • Compared with 2D MRCP, 3D DL-CS-MRCP had superior performance in SNR and CNR, better visualization of the left second-level intrahepatic bile ducts, and comparable overall image quality, but an inferior main pancreatic duct. [ABSTRACT FROM AUTHOR]