BACKGROUND The aim of this study was to evaluate the diagnostic potential of magnetic resonance cholangiopancreatography (MRCP) in preoperative patients with secondary common bile duct stones during the application of laparoscopic trans-cystic common bile duct exploration (LTCBDE). METHODS The clinical records of 255 patients were retrospectively analyzed. All patients included in the study were examined by MRCP 3 days prior to LTCBDE. RESULTS Secondary bile duct stones were detected in 220 patients using LTCBDE. Of the patients diagnosed by MRCP, 141 were true-positive, 28 were true-negative, 7 were false-positive and 79 were false-negative. The sensitivity, specificity, accuracy, positive predictive value, and negative predictive value of MRCP for secondary common bile duct stones were 64.09%, 80.00%, 66.27%, 95.27%, and 26.17%, respectively. When the cases with muddy stones were excluded, the outcomes were 80.41%, 79.41%, 69.23%, 94.44%, and 48.21%, respectively. When cases with stones <3 mm (inclusive) in diameter were excluded, the outcomes were 93.75%, 79.41%, 86.27%, 93.75%, and 65.85%, respectively. When cases with stones <5 mm (inclusive) in diameter were excluded, the outcomes were 93.10%, 79.41%, 89.26%, 92.05%, and 81.82%, respectively. CONCLUSIONS The effectiveness of preoperative MRCP is overestimated for the diagnosis of secondary common bile duct stones, particularly for muddy and micro-stones.