Cerebral venous sinus thrombosis (CVT) becomes the cause of stroke in less than 1% of patients. In 20-30% of patients, the cause of thrombosis remains unclear, and thrombosis is considered idiopathic. Inherited hypercoagulable conditions significantly increase the risk of CVT. The aim of the study was to evaluate the frequency of prothrombogenic polymorphic variants of hemostatic and methionine-homocysteine metabolism genes alleles and genotypes in patients with aseptic CVT. Fifty one patients aged 18–75 with aseptic CVT were examined. The control group included 36 healthy volunteers. Neuroimaging methods included brain MRI in standard modes (T1, T2, T2 d-f (FLAIR), DWI) and MR venosinusography. All patients were surveyed to identify carriers of prothrombogenic polymorphic variants of hemostatic and folate metabolism genes alleles and genotypes. Prothrombogenic polymorphic variants of hemostatic genes were detected in 94% of patients, and the variants of the methionine-homocysteine metabolism genes were observed in 86% of patients. The differences between distributions of alleles and genotypes 5G6754G of the PAI-1 gene, G103T of the FXIIIA1 gene, A66G of the MTRR gene, A2756G of the MTR gene in the group of patients with CVT and in the control group were significant. Allele 4G, genotypes 4G/4G and 5G/4G of 5G6754G polymorphism of the PAI-1 gene; allele T of G103Т polymorphism of the FXIIIA1 gene; allele G and genotype A/G of A66G polymorphism of the MTRR gene; allele G and genotype A/G of A2756G polymorphism of the MTR gene correlated with aseptic CVT. It was concluded that the gene polymorphisms 5G6754G (PAI-1), G103T (FXIIIA1), A66G (MTRR) and A2756G (MTR) carriage increased the risk of aseptic CVT and did not affect the thrombosis clinical manifestations.