Objective: The mortality of right heart thrombi (RHT) associated with pulmonary embolism (PE) is increased about three to four times. The most devastating scenario is fragmentation of RHT and occurrence of recurrent PE. The reports regarding the management of RHT complicated with PE are very scarce in the current literature. Therefore, we report a single-center experience in this paper. Methods: From January 2006 to December 2011, data of all patients diagnosed with acute PE were analyzed retrospectively. Of the 312 acute PE cases confirmed with computed tomography, total 35 patients who were diagnosed with concomitant RHT (prevalence of 11%) by echocardiography were recruited. After excluding of six patients with metastatic malignancy a total 29 patients were accepted eligible for the analysis. In addition, catheter -induced thrombus (type B) were not included to the study. The difference between categorical variables was analyzed with Chi-square test and continuous variables were analyzed with Mann-Whitney U test. A p value of <0.05 was considered statistically significant. Results: Overall mortality was high (34%) in study population: among undergoing surgery-100%, therapy with thrombolytics -18%, and heparin -27%. Troponin levels were found significantly higher in died patients than that in survived patients (p=0.03). There was no significant difference regarding to clinical and echocardiographic characteristics of patients received heparin versus thrombolytic except for shock index (p=0.02). In addition, patients treated with heparin had increased duration of hospitalization compared to subjects treated with thrombolytic (median: 8 vs 3 days p<0.01). Conclusion: Despite of the low incidence of RHT, a mortal course is still an important problem during PE. The decision on treatment modality should be performed based on the hemodynamic parameters, laboratory findings, and bleeding risk of the patients.