Report of right atrial thrombus complicating pulmonary embolism after cardiac surgery is rare. A 54-year-old woman operated on the atrial septal defect 10 months ago was admitted for left pleuritic pain and dyspnea. Multiple segmental perfusion defects were detected in lung perfusion scan. Transesophageal echocardiography showed a large mobile right atrial mass attached to the free wall of the right atrium with a stalk. Despite the intravenous heparinization for 13 days, follow-up echocardiography revealed the right atrial mass had not diminished in size. The mass which was confirmed as an organizing thrombus was excised under cardiopulmonary bypass. The patient recovered uneventfully and was discharged on warfarin therapy.