The data on the risk factors and etiology of ischemic stroke in 31 infants, aged under 3 years, are summarized. The results of genotyping of blood coagulation and folic acid gene polymorphisms in patients and 83 healthy people are presented. Significant differences were found for -455 G>A FGB (р=0.03) and 807 C>T ITGA2 (р=0,005) polymorphisms. Different gene-gene combinations that can cause hypercoagulation and arterial thrombosis in this age were identified. The most frequent combinations include polymorphisms of genes for FGB, fibrinolysis system and folate cycle enzymes (OR=3,79 and more, p<0.05). A clinical case of ischemic stroke in a girl, aged 10 months, after operated congenital heart malformation is presented.