The aim of this study was to evaluate the significance of factor V (FV) G1691A, prothrombin G20210A, methylenetetrahydrofolate reductase (MTHFR) C677T, and plasminogen activator inhibitor-1 (PAI-1) 4G/5G genotypes in development of childhood cerebral thrombosis (CT). A total of 113 Turkish children with CT were studied and compared with the control group. The carrier frequency of the factor V G1691A mutation was found to be significantly higher in the patient group (17.7%) than controls (7.4%). The presence of this genotype was associated with a 2.7-fold increased risk of developing CT (95% confidence interval [CI], 1.0-7.0). The prevalence of prothrombin G20210A mutation in 110 patients (4.5%) was insignificantly higher than controls (2.3%) (odds ratio, 2.0; 95% CI, 0.4-10.7). A statistically significant increase in the frequency of homozygous MTHFR C677T genotype was observed in 62 patients (11.3%) compared to controls (4.3%), and this genotype was associated with 2.8-fold increased CT risk (95% CI, 1.0-8.0). The incidence of PAI-1 4G/4G genotype in 65 patients (21.5%) was slightly lower than that of controls (26.0%), but the differences did not reach statistical significance (odds ratio, 0.8; 95% CI, 0.4-1.5). The results of this study suggested that factor V G1691A and MTHFR C677T genotypes may be associated with an increased risk of developing CT in Turkish children.