BACKGROUND AND OBJECTIVES: There is a lack of consensus about the optimal noninvasive strategy for patients with suspected choledocholithiasis. Two previous systematic reviews used different methodologies not based on pretest probabilities that demonstrated no statistically significant difference between Endoscopic ultrasound (EUS) and magnetic resonance cholangiopancreatography (MRCP) for the detection of choledocholithiasis. In this article, we made a comparison of the diagnostic ability of EUS and MRCP to detect choledocholithiasis in suspected patients. METHODS: We conducted a systematic review in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) recommendations with all published randomized prospective trials. We performed the systemic review using MedLine, EMBASE, Cochrane, LILACS, and Scopus reviews through May 2015. We identified eight randomized, prospective, blinded trials comparing EUS and MRCP. All the patients were submitted to a gold standard method. We calculated the study-specific variables and performed analyses using aggregated variables such as sensitivity, specificity, prevalence, positive predictive value (PPV) and negative predictive value (NPV), and accuracy. RESULTS: Five hundred and thirty eight patients were included in the analysis. The pretest probability for choledocholithiasis was 38.7. The mean sensitivity of EUS and MRCP for detection of choledocholithiasis was 93.7 and 83.5, respectively; the specificity was 88.5 and 91.5, respectively. Regarding EUS and MRCP, PPV was 89 and 87.8, respectively, and NPV was 96.9 and 87.8, respectively. The accuracy of EUS and MRCP was 93.3 and 89.7, respectively. CONCLUSIONS: For the same pretest probability of choledocholithiasis, EUS has higher posttest probability when the result is positive and a lower posttest probability when the result is negative compared with MRCP.