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Besides pulmonary arteriography, a number of imaging techniques, such as magnetic resonance imaging (MRI) and computed tomography (CT), were adopted in the detection of identifying pulmonary embolism (PE). However, the contrast of sensitivity and specificity in these methods was studied little in a statistical way. To compare the effects of MRI and CT, this study used a series of methods to analyze data in included researches.A comprehensive computer search was conducted through internet up to July 2016. The quality assessment was performed by the Quality Assessment Tool for Diagnostic Accuracy Studies, version 2 tool. The diagnostic value of comparison between MRI and CT was evaluated by using the pooled estimate of sensitivity, specificity, and summary receiver operating characteristic (SROC) curve. In addition, sensitivity analysis and bias analysis were applied to ensure the accuracy of the results.Ten studies with 590 cases were involved in the study. Only 2 trials had high risk regarding bias while other trials were supposed to be at low risk of applicability. Heterogeneity existed in analysis of both CT and MRI. The pooled sensitivity of CT was 0.90 (95% CI: 0.85–0.93), pooled specificity was 0.88 (95% CI: 0.77 to 0.95), the pooled sensitivity of MRI was 0.92 (95% CI: 0.89–0.94), and pooled specificity was 0.91 (95% CI: 0.77–0.97). The Q index of sensitivity and specificity for CT and MRI were 71.38, 19.67, 47.14, and 12.35, respectively. The SROC curve area under the curve of CT and MRI were 0.94 (95% CI: 0.91–0.96) and 0.93 (95% CI: 0.91–0.95), respectively.This meta-analysis demonstrates that MRI has better sensitivity and specificity in detecting subsegmental artery PE. MRI is a relatively better detection technique for PE. This conclusion is consistent with many published researches.