Diffusion- and perfusion-weighted magnetic resonance imaging (MRI) was used to study the putative effects of apolipoprotein E (ApoE) polymorphism in stroke. Thirty-one patients with acute stroke, comparative for age and gender were scanned, nine of whom were ApoE allele epsilon 4 carriers. Initially, less than 24 hours from the onset of stroke, the epsilon 4 carriers had significantly smaller volumes of hypoperfusion on relative cerebral blood volume map (P = 0.001), and smaller infarct volumes (P = 0.008) compared with the noncarriers. By day 8, this difference in the infarct volumes had disappeared, suggesting relatively enhanced infarct growth. On average, the total infarct volume increased 145% of the initial infarct volume in the epsilon 4 carriers, and 84% in the noncarriers. There were strong correlations between the imaging findings and clinical status initially and with the outcome 3 months after the stroke in the epsilon 4 noncarriers, but, with a single exception at acute phase, a lack thereof in the epsilon 4 carriers. These patterns were virtually similar in a subgroup of patients with middle cerebral artery stroke. These data support the hypothesis of increased general vulnerability of the brain in the epsilon 4 carriers. Thus, the effects of ApoE polymorphism should be accounted for when interpreting diffusion- and perfusion-weighted MRI studies, particularly if predicting lesion growth.