Transesophageal echocardiography (TEE) is more sensitive than transthoracic echocardiography (TTE) in detecting the potential source of emboli in cardioembolic strokes (CES). To establish the prevalence of a potential cardiac source of embolism detectable on TEE and its relationship to vascular risk factors, an unselected ischemic stroke population was evaluated. Twenty-six age and sex-matched cases with normal cardiological and neurological examinations as well as normal CT-scans, TTE and ECGs were included in the study as the control group. One hundred and eight patients with cardioembolic stroke (53 patients), atherothrombotic stroke (36 patients), and lacunar stroke (19 patients) were investigated by TTE and TEE. Seven of the 26 (26.9%) controls had thoracic atherosclerotic plaques on TEE examinations. The prevalence of abnormal TEE findings in patients was higher compared to the controls (p < 0.001). TEE revealed more specific findings in every etiological group when compared to TTE (74.0% vs 10.2%, p < 0.001). Atrial fibrillation correlated with the abnormalities of TEE (p < 0.05) while other risk factors did not. Left atrial spontaneous echo contrast was the most common finding on TEE of cases with cardioembolic stroke while atherosclerotic aortic plaques were mostly encountered in patients with atherothrombotic stroke. No specific findings by TEE were seen in patients with lacunar stroke. TEE is capable of detecting definite etiologies in cardioembolic stroke and associated cardiac pathologies in atherothrombotic stroke and lacunar stroke. These observations suggest that TEE is a useful tool to guide the physician for the treatment of ischemic stroke patients.