A 68-year-old man was admitted to our hospital with dyspnea and general fatigue. At first, pulmonary embolism was diagnosed by electrocardiography and pulmonary scintigram. X-ray CT scans and echocardiography revealed a tumor occupying the right atrial cavity. To prevent further pulmonary embolism, he underwent tumor resection. In surgery, two venous drainage cannulas were inserted directly to the superior vena cava and to the inferior vena cava via the right femoral vein, in order to avoid the direct contact with the right atrium prior to institution of extra-corporeal circulation. The tumor was carefully removed together with the atrial wall around the site where the tumor originated. A pathological study showed that the specimens were myxoma in the right atrium. His post-operative course has been uneventful until now, however, long-term observation with respect to the metastasis and/or recurrence of this tumor will be carried out.