Intracardiac thrombus during cardiopulmonary bypass (CPB) with full heparinization is very rare but fatal. A 60-year-old woman was scheduled for aortic and mitral valve repairs with a maze procedure for mixed aortic and mitral valvular heart disease with atrial fibrillation. Preoperative transthoracic echocardiography and cardiac computed tomography showed moderate aortic regurgitation and moderate mitral stenosis with regurgitation. There was no intracardiac thrombus. Aortic and mitral valve repairs with the maze procedure were successfully performed without unexpected events. During CPB weaning, a mobile hyper-echogenic mass in the left atrium was detected on transesophageal echocardiography. After cardiac arrest, it was surgically removed. On completion of the operation, weaning from CPB was accomplished uneventfully. The patient fully recovered and was discharged from the intensive care unit on her third postoperative day.