A 53-year-old man with a history of repair of atrial septal defect 3-months ago by primary suture was admitted to an emergency department with sudden onset chest pain and dyspnea. Transthoracic echocardiography revealed a large and mobile thrombus attached to the right side of the interatrial septum. The chest X ray and perfusion lung scan established the diagnosis of the multiple pulmonary emboli. Doppler examination of the venous system for a possible source of thrombus was unremarkable. The postoperative early appearance of thrombus and multiple pulmonary emboli defects at lung scan supported that thrombus was originated from the primary suture site. Thrombolytic treatment achieved complete resolution of the thrombus both in the pulmonary artery and at the repaired septal defect site. The patient was placed on warfarin and thrombus was not detected by transesophageal echocardiography at the 9-month follow-up.