A 70-year-old man was admitted with sudden onset of dyspnea, near syncope and left hemiparesis. Clinical examination, blood gas analysis, ECG and the chest X-ray were consistent with pulmonary embolism. Transthoracic echocardiography (TTE) revealed right atrial free-floating thrombus, large atrial septal defect (ASD), right heart enlargement and pulmonary artery hypertension. Anticoagulation therapy was initiated immediately, soon after thrombolytic therapy was started but the patient died due to possible pulmonary or cerebral embolization. We underscore rapid diagnosis by TTE that revealed right heart thrombus in transit and large ASD.