AbstractAim:  To determine whether factor V Leiden (FVL) and prothrombin (PT) 20210G>A mutation are associated with paediatric ischaemic stroke.Methods:  The study consisted of two parts. Case–control study included neuroradiologically confirmed paediatric ischaemic stroke patients from two tertiary children’s hospitals in Estonia. For control group, DNA was obtained from 400 anonymous screening test cards of newborns born consecutively in all delivery departments of Estonia in January 2005. Meta‐analyses was performed to assess the association between paediatric sinovenous thrombosis and FVL and PT 20210G>A.Results:  A total of 75 children (45 boys, 30 girls) were included into the case–control study: 19 with childhood arterial ischaemic stroke, 49 with perinatal arterial ischaemic stroke and seven with cerebral venous thrombosis. Both FVL and PT 20210G>A occurred significantly more frequently among patients with sinovenous thrombosis compared with controls (OR = 12.9; 95% CI: 2.3–73.0 and OR = 11.9; 95% CI: 2.1–67.2, respectively). The difference was not significant between childhood/perinatal arterial ischaemic stroke and controls. Meta‐analyses (including our study) revealed that both FVL and PT 20210G>A are associated with paediatric sinovenous thrombosis (OR = 3.1; 95% CI: 1.8–5.5 and OR = 3.1; 95% CI: 1.4–6.8, respectively).Conclusion:  FVL and PT 20210G>A are associated with paediatric sinovenous thrombosis.