We evaluated associations between cerebral blood flow (CBF) and histopathological features in atherosclerotic lesions of the internal carotid artery. Cerebrovascular reactivity (CVR) and CBF were measured in 72 patients with unilateral carotid artery stenosis who underwent Xe-CT before carotid endarterectomy. Collateral blood flow was estimated as stump pressure. Proportions of fibrous tissue, intraplaque hemorrhage (IPH), and calcification were pathologically compared with the entire plaque body. The Spearman's rank test and stepwise multiple linear regression analysis revealed that the IPH rate significantly and negatively correlated with CBF, whereas the calcification rate positively correlated with CVR. One-way analysis of variance showed that IPH and the absence of calcification might confer a risk for CBF and CVR reduction. Thus, not only the stenosis rate but also the degree of IPH and calcification in carotid arterial plaque are notable risk factors for ischemic stroke.