There is a lack of consensus on the optimal noninvasive strategy for patients with suspected choledocholithiasis after a negative transabdominal ultrasound and/or computed tomography. A meta-analysis was conducted to compare the diagnostic ability of endoscopic ultrasound (EUS) and magnetic resonance cholangio-pancreatography (MRCP) in patients with suspected common bile duct (CBD) stones. A search, using the following terms 'MRCP', 'EUS' and 'Choledocholithiasis' in Pubmed and Cochrane Controlled Trials Register, was performed. Abstract books and reference list of review articles, as well as relevant studies, were also searched to complete our EUS versus MRCP for choledocholithiasis comparison studies database. The analysis demonstrated that, with respect to sensitivity, specificity and accuracy, there was no statistically significant difference between EUS and MRCP for the detection of choledocholithiasis. Our meta-analysis of prospective comparison of MRCP and EUS for the detection of choledocholithiasis yielded statistically similar diagnostic values for both techniques.