We report a case of vanished thrombus in the ascending aorta whose disapperance was confirmed by using the intraoperative epi-aortic echocardiography. The thrombus was found coincidentally at the examination of a malignant tumor. We determined that thrombus removal was necessary for the risk of embolism owing to their mobility. We planned surgical removal of the thrombus accompanied graft replacement for the ascending aorta, however, the thrombus had already vanished at the time of the operation. Following computed tomography revealed that the vanished thrombus did not cause any embolism.