Ankle brachial index (ABI) and brachial-ankle pulse wave velocity (baPWV) are widely used noninvasive modalities to evaluate atherosclerosis. Recently, evidence has increased supporting the use of ABI and baPWV as markers of cerebrovascular disease. This study sought to examine the relationship between ABI and baPWV with ischemic stroke. This study also aimed to determine which pathogenic mechanism, large artery disease (LAD) or small vessel disease (SVD), is related to ABI or baPWV. Retrospectively, 121 patients with ischemic stroke and 38 subjects with no obvious ischemic stroke history were recruited. First, ABI and baPWV were compared between the groups. Then, within the stroke group, the relevance of ABI and baPWV with regard to SVD and LAD, which were classified by brain magnetic resonance image (MRI) and magnetic resonance angiography (MRA) or computed tomography angiography (CTA) findings, was assessed. The baPWV was higher in the stroke group than non-stroke group (1,944.18±416.6 cm/s vs. 1,749.76±669.6 cm/s, P<0.01). Regarding LAD, we found that mean ABI value was lower in the group with extracranial large artery stenosis (P<0.01), and there was an inverse linear correlation between ABI and the grade of extracranial large artery stenosis (P<0.01). For SVD, there was a significant correlation between SVD and baPWV (2,057.6±456.57 cm/s in the SVD (+) group vs. 1,491±271.62 cm/s in the SVD (-) group; P<0.01). However, the grade of abnormalities detected in SVD did not correlate linearly with baPWV. These findings show that baPWV is a reliable surrogate marker of ischemic stroke. Furthermore, baPWV and ABI can be used to indicate the presence of small vessel disease and large arterial disease, respectively.