A patient with mitral stenosis and multiple left atrial thrombi underwent valvuloplasty and thrombectomy. While closing the sternum after completing the cardiopulmonary bypass, a new left atrial thrombus was detected by transesophageal echocardiography. We used heparin for the prevention of new thrombus formation and closed the wound after meticulous bleeding control. Three months later, there was no residual thrombus in the left atrium according to the echocardiographic study.