The aim of this study was to clarify the usefulness of magnetic resonance cholangiopancreatography (MRCP) for the evaluation of choledochal cyst in children.MRCP was performed preoperatively in 33 patients. The MRCP findings were compared with those of endoscopic retrograde cholangiopancreatography or intraoperative cholangiopancreatography.In all 33 patients, MRCP could detect choledochal cyst. The detection rate of a cyst in the main pancreatic duct was 62.2%, of abnormal union of the pancreaticobiliary junction (AUPBJ) was 53.3%, of dilatation or abnormalities of the main pancreatic duct was 75.0% and of a protein plug or stone was 76.9%. In patients under 2 years of age (group A), these findings were significantly lower than those of patients above 2 years of age (group B) [main pancreatic duct: 16.6% (1/6) vs 73.1% (19/26), P0.01; AUPBJ: 0.0% (0/6) vs 66.7% (16/24), P0.05; and protein plug or stone: 0.0% (0/2) vs 90.9% (10/11), P0.05]. The detection rate of AUPBJ in the patients with fusiform dilatation was superior to that of those with cystic dilatation [70% (14/20) vs 20% (2/10), P0.05]. In the patients with fusiform dilatation, the detection rate in group A was significantly lower than that in group B [0.0% (0/3) vs 82.4% (14/17), P0.01]; however, there was no significant difference between the 2 groups in the detection of cystic dilatation.In patients older than 2 years, MRCP should be the first-choice method for confirming the diagnosis and for ensuring accurate visualization of the pancreaticobiliary system.