We describe a case of right atrial myxoma in a 62-year-old woman presenting with syncope. The patient had a 4-month history of syncope and felt faint on lying flat in bed before the admission. Transthoracic and transesophageal echocardiography showed a large right atrial mass that was prolapsing through the tricuspid valve into the right ventricle during diastole. Coronary angiography revealed a tumor stain through the right coronary artery and no significant stenosis of the coronary arteries. During operation, cardiopulmonary bypass was initiated with cannulation into the aorta and retrograde femoral vein and superior vena caval cannulation. The large tumor was attached by a short stalk to the interatrial septum at the border of the fossa ovalis. The tumor and the interatrial septum including the stalk with a 1.5-2.0 cm cuff extending the full thickness of the septum were completely excised. A histologic examination of the tumor confirmed the diagnosis of cardiac myxoma. We emphasize a characteristic feature of syncopal attacks, and discuss the importance of prevention of intraoperative systemic and pulmonary tumor embolization resulting from venous cannulation for cardiopulmonary bypass in patients with right atrial myxomas.