Ischemic stroke is a multifactorial disease leading to severe long-term disability and it is the third leading cause of death in developed countries. Although many studies have been reported to elucidate etiological and pathological mechanisms of stroke, the genetic and molecular basis of disease remains poorly understood. Recent studies have shown that reactive oxygen species causing oxidative stress play a pivotal role in the pathogenesis of atherosclerosis that is the main cause of a group of cardiovascular diseases including ischemic stroke. In this study, we aimed to investigate the relationship between FMO3 Glu158Lys and Glu308Gly variants, and the risk of incidence of ischemic stroke in Turkish population. Two single nucleotide polymorphisms (SNPs) within the PMO3 gene were genotyped by using PCR-RFLP technique in a sample set of 245 cases and 145 controls. In the case-control analysis, no significant difference was observed between stroke patients and controls with respect to FMO3 Glu158Lys and Glu308Gly polymorphisms' genotype and allele frequency distribution. However, heterozygote 158Glu/Lys (OR = 6.110, P < 0.001) and 308Glu/Gly (OR = 6.000, P = 0.006) genotypes increase the risk of stroke 6 times in hypertensive subjects. On the other hand, the wild type genotypes 158Glu/Glu and 308Glu/Glu had 6.2-fold and 4.8-fold higher risk of ischemic stroke in obese subgroup, respectively. Our results clearly showed that the risk of hypertension-related ischemic stroke was higher in the heterozygote genotype carriers. This is the first study conducted regarding the association of FMO3 Glu158Lys and Glu308Gly genetic polymorphisms and ischemic stroke risk in Turkish population. (C) 2013 Elsevier B.V. All rights reserved.