Apolipoprotein E-(apoE) deficient mice exhibit hypercholesterolemia, accelerated atherosclerosis and increased infarct size after middle cerebral artery occlusion (MCAO). This study examined whether worsened ischemic outcome is attributable to effects of apoE deficiency on cerebral circulation. Wild type and apoE-deficient mice underwent MCAO and autoradigraphic measurement of cerebral blood flow. Circle of Willis anatomy was examined in non-ischemic animals. Both groups exhibited similar reduction in blood flow. Both groups had 100% incidence of filling of the anterior communicating artery. The posterior communicating artery (PcomA) filled in 70% of wild type and 80% of apoE-deficient mice. Both groups had considerable variability in relative sizes of the PcmA. This study indicates that worsened outcome from MCAO of apoE-deficient mice is not attributable to any detectable vascular effects and offers validity to use of apoE-deficient mice for study of apoE as a factor in cerebral ischemic pathophysiology.