Objective To investigate the prognostic value of B-type natriuretic peptide (BNP) for short-term all-cause mortality in patients with acute pulmonary embolism (APE). Methods Such databases as PubMed, EMbase, Central Register of Controlled Trials, CBM, and CNKI (from the date of their establishments to March 2010) were searched. The level of BNP and N-terminal pro-B-type natriuretic peptide (NT-proBNP) was collected to conduct eligible cohort study for assessing their effects on APE prognosis. Quality assessment and data extraction were performed in those clinical trials in line with the inclusion criteria. Then, RevMan 5.0 software was applied to carry out meta-analyses. Results Sixteen relevant studies with 1 126 APE patients were included. Nine studies reported BNP level and seven studies reported NT-pro BNP level. There was less satistical and clinical Heterogeneity among the groups (P=0.94, I2=0; P=0.99, I2=0). The meta-analyses results showed: the BNP or NT-pro BNP level was closely related with the short-term all-cause mortality. SPE was 0.52, + LR was 1.87, –LR was 0.20, PPV was 0.16, NPV was 0.98, SROC area under the curve was 0.830 5, SE (AUC) = 0.033 5.Conclusion While elevated BNP levels can help to identify APE patients at a higher risk of death, the high negative predictive value of normal BNP levels is more useful for doctors to identify patients with less likelihood of adverse events so as to conduct a selective follow-up.