Genetic factors can account for the differences in the frequency of stroke between men and women. Despite the scarcity of special clinico-genetic studies of stroke frequency in the two genders, analysis of association between DNA polymorphism and risk of stroke may reveal the influence of genetic factors on the sex-related predisposition to cerebrovascular diseases. The present work was aimed to study the relationship between frequent polymorphisms -786T > C of endothelial nitric oxide synthase (NOS3) gene E298D and the risk of stroke in men and women. 904 DNA samples were obtained from unrelated Russian residents of Central Russia including 480 stroke patients and 424 healthy volunteers. Genotyping was performed by PCR in real time with allele discrimination using TaqMan probes. The homoygous genotype of NOS3 gene E298D was found to be associated with an increased risk of stroke in men (OR 2.60; 95% CI 1.28-5.29, p = 0.01). Neither men nor women showed association of polymorphism -786T > C with the predisposition to stroke. The E298D genotype in men was associated with the enhanced risk of both ischemic (OR 2.38; 95% CI 1.14-4.96, p = 0.02) and hemorrhagic (OR 5,58; 95% CI 1.95-16.05, p = 0.003) stroke. Thus, NOS3 gene E298D polymorphism is a reliable predictor of predisposition to various pathogenetic variants of stroke only in men.