The association between apolipoprotein E (ApoE) polymorphism and stroke is still controversial. This study investigated the potential association between ApoE genotypes and stroke subtypes, and risk factors for ischaemic stroke in Greek patients hospitalized with their first-ever ischaemic stroke. One hundred patients (70 men and 30 women; mean age +/- SD 60.7 +/-9.8 years) were included in the study. The control group comprised 96 age- and sex-matched healthy volunteers. Cerebral infarction was classified as atherothrombotic, cardioembolic or lacunar small-vessel stroke. The three common ApoE alleles (E2, E3 and E4) were determined using the semi-nested polymerase chain reaction. No significant difference in the ApoE alleles was found between patients and controls. Similarly, there was no significant association between ApoE alleles and stroke subtypes, common risk factors for ischaemic stroke and neck vessel stenosis. Although the sample size was small, these results do not support a role for ApoE polymorphism in the pathogenesis of ischaemic stroke.