Objective: To evaluate the severity of acute pulmonary embolism (APE) patients by cardial troponin T(c-Tn-T) and brain natriuretic peptide(BNP) and explore its prognostic value. Methods: From January 2005 to July 2009,251 patients diagnosed with APE were enrolled in this study. The level of c-Tn-T and BNP,PaO2 and PaCO2,heart doppler index and clinical outcomes situation were collected. According to the results of PaO2 and PaCO2,patients of APE were divided into three groups. We compared differences between groups and analyzed the correlation. According to the clinical outcome,patients of APE were divided into good outcome group and bad outcome group. We compared the differences between two groups of c-Tn-T,BNP,PaO2,PaCO2 and the predictive values from c-Tn-T and BNP. Results: Along with serious degree of APE increased,c-Tn-T and BNP index significantly increased,and the right cardiac insufficiency significantly increased with statistically significant difference (P < 0.05). Right ventricular enlargement was positively correlated with c-Tn-T and BNP (r = 0.614,P = 0.001;r = 0.598,P = 0.005);Systolic ventricular septal retrorse motion positively correlated with BNP(r = 0.791,P = 0.000);Pulmonary hypertension positively correlated with c-Tn-T (r = 0.711,P = 0.000). To the group with bad outcome,the c-Tn-T,BNP,PaO2,PaCO2 and right cardiac insufficiency were obviously poorer than the group with good outcome (P < 0.05). ROC curves analysis showed that the area under curve(AUC) were large in the curve of the BNP and c-Tn-T. The optimum operating point for c-Tn-T and BNP were 0.94 ng/ml and 458.12 pg/ml,respectively. Conclusion: c-Tn-T and BNP can assess severity of disease for APE patients. At the same time,they also provide an objective basis for clinical treatment and prognosis assessment.