Ischemic stroke (IS) is a multifactorial disease caused by the interaction of genetic and environmental factors. The question of whether mild hyperhomocysteiemia (Hcy) is a risk factor for CVD has been debated and is still unclear. Common single nucleotide polymorphisms (C677T and A1298C) in the methylenetetrahydrofolate reductase gene (MTHFR) decrease the activity of the enzyme, leading to hyperhomocysteinemia, particularly in folate-deficient states. We investigated whether there is a link between MTHFR gene C677T and A1298C polymorphisms or plasma homocysteine and IS.Patients and methods: Genotypic analyses were performed on 308 consecutive unrelated patients diagnosed with IS, 147 women and 161 men, mean age 700.8 years, who were diagnosed according to the Trial of Org 10172 in Acute Stroke Treatment. All included cases were age and sex matched to a control from the same geographic area who had no history of vascular disease. Patients and controls completed a questionnaires including blood pressure, diabetes status, total serum cholesterol level and smoking history. Genetic tests were performed by RFLP-PCR and homocysteine levels in plasma were measured by ELISA method. The strength of the association of the polymorphisms with the occurrence of IS was estimated by calculation of the OR and its 95%CI by exact method. P values less than 0.05 were considered significant. Logistic regression analysis was applied to estimate the risk in a multivariable predictive model with dependent variable (case/control) and all independent variables significant in the bivariate analysis. SPSS 9.0 was used for the statistical analysis.Results: The distribution of MTHFR gene C677T genotypes in patients (or controls) was: CC-genotype in 134 cases, 44.1% (155 controls, 50.5%); CT-genotype in 131 cases, 43.1% (138 controls, 44.9%); and TT-genotype in 39 cases, 12.8% (14 controls, 4.6%). The distribution of MTHFR gene A1298C genotypes in patients (or controls) was: AA-genotype in 164 cases, 55.6% (127 controls, 41.2%); AC-genotype in 113 cases, 38.3% (149 controls, 48.4%); and CC-genotype in 18 cases, 6.1% (32 controls, 10.4%). Genotype analysis showed a significant higher prevalence of the TT-genotype of MTHFR C677T in patients (p= 0.001;OR= 3.08;95%CI= 1.63–5.79). Nevertheless, genotype analysis showed a lower prevalence of the CC genotype of MTHFR A1298C in patients (p= 0.056;OR= 0.56;95%CI= 0.3–1.02). The genetic analysis was similar for the different subtypes of IS. Homocysteine plasma level was significantly higher in homozygosity for 677T allele than wild type (20.2±9.3 mmol/l and 17.4±6.5 mmol/l; p=0.029) and was lower in homozygosity for 1298C allele than wild type (16.2±5.7 mmol/l and 18.7±9.0 mmol/l; p=0.029). Homocysteine plasma levels in doubly heterozygous for C677T and A1298C mutations in the MTHFR gene were higher than the other genotypes (20.6±8.4 mmol/l and 18.6±8.3 mmol/l; p= 0.133). Logistic regression analysis showed a independent association of 677T allele of MTHFRwith CVD. Also hypertension, diabetes mellitus and current smoking status were statistically associated with CVD.Conclusions: Our findings suggest that the T allele of 677 MTHFR polymorphism is a genetic risk factor for IS in Spanish population. The unexpected protective effect of the 1298C allele of 1298 MTHFR polymorphism for IS needs further study. Supported by Grant FIS 03/0176. Oa R: Fundacion Conchita Rabago Grant. Santos AB: Fundacion LAIR 2004 Grant.