Protruding atheromas of the aorta have been identified as one of the sources of a systemic emboli and a major cause of stroke following cardiac surgery. We report a case of surgical modification in a 58-year-old man with an atheromatous aortic arch detected by an intraoperative transesophageal echocardiography (TEE) during coronary artery bypass grafting (CABG). After induction of anesthesia, protruding atheromatous plaques with a mobile element in the aortic arch were identified by a TEE that was not noticed by a preoperative angiography and transthoracic echocardiograpy. Based on the TEE finding, the surgical technique was modified to CABG combined with an aortic atherectomy under deep hypothermic circulatory arrest. The atheromatous areas correlated well with the TEE finding and the patient recovered from anesthesia and surgery without neurologic deficit. Therefore, an intraoperative TEE examination is considered as a safe and reliable technique to identify atherosclerotic disease of the thoracic aorta in patients undergoing CABG and to minimize unexpected neurologic complications after CABG.