Objective 20-Hydroxyeicosatetraenoic acid has been shown to play an important role in cerebral vascular function. We hypothesized that polymorphisms in genes encoding 20-Hydroxyeicosatetraenoic acid synthesizing enzymes might confer susceptibility to stroke. Methods and results To test the hypothesis, haplotype tagging single nucleotide polymorphisms and potential functional polymorphisms of CYP4A11 and CYP4F2 genes were genotyped in 558 ischemic stroke patients, 221 hemorrhagic stroke patients and 557 controls. The association analyses were performed at both single nucleotide polymorphism and haplotype levels. We further verified our findings in an independent cohort of 551 ischemic stroke cases and 48 hemorrhagic stroke cases and 694 unaffected controls. We identified CYP4A11 C-296T and CYP4F2 V433M were associated with significantly increased risk of ischemic stroke (CT + TT vs. CC, adjusted odds ratio: 1.50, 95% confidence interval: 1.17-1.93, P-combined = 0.001, P-corr = 0.008; V/M + M/M vs. V/V, odds ratio: 1.38, 95% confidence interval: 1.15-1.65, P-combined = 5.6 x 10(-4), P-corr = 0.005, respectively). Interestingly, the effects of CYP4F2 V433M on ischemic stroke in our study was only evident in male individuals. Conclusion Our results suggest that genetic variation in CYP4A11 and CYP4F2 alters susceptibility to stroke in the Han Chinese population. Pharmacogenetics and Genomics 20:187-194 (C) 2010 Wolters Kluwer Health vertical bar Lippincott Williams & Wilkins.