Aim. To analyze the relationships between the carriage of polymorphic variants in the folate metabolism genes and the development of thrombotic complications in patients with single ventricle (SV) during surgical treatment.Material and Methods. A total of 102 children with SV were examined in the performed research. All patients underwent surgical hemodynamic correction of congenital heart disease (CHD). According to a retrospective chart review, thrombosis was diagnosed in 12.7 % of the examined patients with SV. The analysis of polymorphism in the MTR A2756G enzyme gene revealed significant differences between the groups of patients with a history of thrombosis and without it.Results. We found that the risk of developing thrombosis was associated with the carriage of homozygous genotype 2756AA of the MTR enzyme gene (OR = 11.21; 95% CI: 1.39–89.96; p = 0.023).