Only coronary artery disease and cancer kill more people than stroke in the United States. Transesophageal echocardiography (TEE) is a semi-invasive ultrasound cardiac imaging technique that provides superior anatomic detail as well as functional information. Searching for a cause of cerebral ischemia is the most common indication for TEE in cardiac ultrasound laboratories. Although TEE is not superior to transthoracic imaging for identifying all sources of cardiac embolism, its ability to more sensitively detect atrial septal aneurysm, patent foramen ovale, and aortic atheroma has been well described in recent years. Care must be exercised in using TEE to identify suspected cardiac sources of embolism, as potential etiologies described in the literature are not equally established by rigorous clinical trials. Confidence level in cause and effect for any cardiac pathology identified must be factored into therapeutic decisions.