Background: Evaluation of coronary artery disease (CAD) and aortic atherosclerosis has been performed in patients with acute ischemic stroke. We investigated the usefulness of a dual-source CT (DSCT) protocol enabling the comprehensive evaluation of CAD and aortic atherosclerosis. The clinical characteristics of those patients who would benefit more from this protocol were investigated based on vascular risk factors, Framingham Risk Score (FRS), and stroke subtype. Methods: Of 469 patients with acute ischemic stroke, the 274 who had no history of CAD and had undergone DSCT were analyzed. Predictors of CAD (≧50% stenosis) or complicated aortic plaque (CAP) were evaluated based on vascular risk factors, FRS and stroke subtype. Results: Of the 274 patients analyzed, asymptomatic CAD (≧50% stenosis) was found in 61 (22.3%) and CAP in 58 (21.2%). Furthermore, the severity of CAD or aortic atherosclerosis was correlated with FRS (CAD, r = 0.291, p < 0.001 and aortic atherosclerosis, r = 0.297, p < 0.001). Additionally, severe CAD and aortic atherosclerosis were independent predictors of each other: CAP for the presence of CAD (≧50% stenosis) [odds ratio (OR), 5.71; 95% confidence interval (CI), 1.94–16.87]; CAD (≧50% stenosis) for the presence of CAP (OR, 4.20; 95% CI, 1.82–9.72). Specific stroke subtypes as well as large-artery atherosclerosis (OR, 5.25; 95% CI, 2.24–12.31) and cardioembolism (OR, 5.22; 95% CI, 1.75–15.60) were associated with the presence of CAP. Conclusions: A comprehensive evaluation protocol for CAD and aortic atherosclerosis may be useful in acute ischemic stroke patients, especially in those with higher FRS or specific stroke subtypes.