The factor V Leiden mutation is the most common hereditary cause of venous thrombosis in our population. In the pediatric population, it has been associated with cerebrovascular thrombosis, cerebral palsy, and prosencephaly in neonates. We present two children with hemiconvulsion, hemiplegia, and epilepsy syndrome in whom the cause is likely attributable to the factor V Leiden mutation. We suggest that patients presenting with hemiconvulsion, hemiplegia, and epilepsy syndrome should be routinely investigated for factor V Leiden, and, if positive, careful consideration should be given to therapeutic and prophylactic anticoagulation as this may improve long-term outcome.