The purpose of this study was to investigate the incidence of subclinical coronary artery disease (CAD) in patients with suspected acute embolic stroke or transient ischemic attack (TIA) using 64-row multi-slice computed tomography (MSCT) and to examine its association with conventional risk stratification. We consecutively enrolled 175 patients (66 ± 13 years, 50% men) suspected to have had embolic stroke/TIA clinically or radiologically, and underwent 64-row MSCT to evaluate for a possible cardiac source of embolism. Both coronary artery calcium scoring (CACS) and coronary CT angiography (CCTA) were concurrently performed based on standard scanning protocols. Patients with a history of angina or documented CAD, and those with significant carotid stenosis were excluded. Atherosclerotic plaques were indentified in 105 (60%) individuals; 37 (21%) had occult CAD of ≥50% diameter stenosis on CCTA. Subjects with and without ≥50% occult CAD on CCTA had similar prevalence of cardiovascular risk factors. Thirty out of 175 (17%) individuals with ≥50% occult CAD would have missed further cardiac testing based on the American Heart association and the American Stroke Association guideline. However, these numbers would be reduced to 2% (4/175) using CACS. In logistic regression analysis, only CACS independently predicted the presence ≥50% occult CAD evidenced by CCTA. Subclinical CAD, including ≥50% stenotic disease, is highly prevalent in patients who had suffered a suspected embolic stroke. The current guideline for further cardiac testing may have limited value to identify patients with ≥50% CAD in this patient population, which can be improved by adopting CACS.