There is evidence that most forms of ischaemic stroke (IS) result from synergistic effects of the modifiable predisposing factors and multiple genes. In the present work, we report results of case-control study of IS association with apolipoprotein E gene (APOE) (promoter and coding polymorphisms) and lipoprotein lipase gene (LPL) (presence/absence of a HindIII cutting site). We studied 107 unrelated patients of Yakut ethnicity (69 men and 38 women, mean age 58.4+/-11.5 years) with first-ever IS in carotid/middle cerebral artery regions. The control group included 101 subjects of the same ethnicity (61 men and 40 women, mean age 57.6+/-11.6 years) free of clinically detectable cerebrovascular disease, and without any history of stroke. A positive association of IS with APOE -427T allele (p=0.0012, OR=3.99) and -427T/T genotype (p=0.0005, OR=4.96) and a negative association with -427C allele (p=0.0012, OR=0.25), -427T/C genotype (p=0.0003, OR=0.18), epsilon2 allele (p=0.018, OR=0.35), epsilon2/3 genotype (p=0.017, OR=0.28) and -491A/-427C/epsilon2 haplotype (p=0.0026, OR=0.18) were observed. For atherothrombotic subgroup the same allele and genotype associations were found plus association with APOE -491A allele (p=0.026, OR=3.98). No reliable IS associations were found with LPL T+495G (HindIII) polymorphism. An association of APOE promoter polymorphisms (A-491T, T-427C) with an IS is shown in our study for the first time. Our study provides evidence for the role of APOE gene as a prognostic genetic marker for IS, especially for its atherothrombotic subtype.