Hyperhomocysteinaemia is associated with an increased risk of arterial vascular disease and thrombosis in adults. Our aim was to study the association of hyperhomocysteinaemia and stroke in children. Since some patients who had suffered a stroke developed seizures and received treatment with anti-epileptic (antifolate) drugs, we also examined the possible interaction between anti-epileptic drugs and hyperhomocysteinaemia. Plasma total homocysteine was measured in 68 children with stroke (23 of the 68 were taking anti-epileptic drugs) and 100 children undergoing anti-epileptic treatment but without history of stroke, and we compared the values with our reference values for similar ages (n = 195). Total homocysteine was determined by high profile liquid chromatography with fluorescence detection. Hyperhomocysteinaemia was defined as a homocysteine concentration above the 95th percentile for the reference values. Significant differences were found in total homocysteine values of children with stroke and those taking anti-epileptic drugs compared with our reference values for similar ages, except for the adolescent group. Total homocysteine values above the 95th percentile for the reference values were found in 36% of patients with stroke and 28% of children on anti-epileptic treatment. Total homocysteine concentrations in the 23 patients with both stroke and anti-epileptic drug treatment were similar to those of untreated patients with stroke in all age groups. In summary, systematic screening for hyperhomocysteinaemia should be included in the protocol to investigate the aetiology of stroke, even in paediatrics. Anti-epileptic treatment in children with stroke may be responsible for the mild hyperhomocysteinaemia observed in some of them. A dietary supplement of folate may be of benefit in children with stroke and in patients taking anti-epileptic drugs.