Genotyping for the methylenetetrahydrofolate reductase gene (MTHFR) has been recommended for part of the evaluation for underlying prothrombotic state in childhood stroke; however, studies are inconclusive regarding the role of this gene and also the role of hyperhomocysteinemia, which is the putative mechanism by which MTHFR polymorphism is related to stroke. The prevalence of MTHFR polymorphism in childhood arterial ischemic stroke and cerebral sinovenous thrombosis was compared with that of a reference population, and prevalence of hyperhomocysteinemia was reviewed. In arterial ischemic stroke, the prevalence of at-risk methylenetetrahydrofolate reductase genotypes was 27%, and in cerebral sinovenous thrombosis it was 13%; the population prevalence was 26%. The odds ratio for at-risk genotype in childhood arterial ischemic stroke was 1.06 (95% confidence interval, 0.22-4.0); in cerebral sinovenous thrombosis, it was 0.42 (95% confidence interval, 0.01-3.6). No tested cases had hyperhomocysteinemia. MTHFR polymorphism and hyperhomocysteinemia were not risk factors in childhood arterial ischemic stroke or cerebral sinovenous thrombosis in the Intermountain West region.