Cytochrome P450 2C19 (CYP2C19) is expressed in human endothelial cells and catalyzes the biosynthesis of vasoprotective epoxyeicosatrienoic acids and 19-hydroxyeicosatetraenoic acid from arachidonic acid. This study investigated the association between CYP2C19 polymorphisms and an increased risk of diabetic retinopathy (DR). A clinic-based retrospective longitudinal analysis was carried out that included 383 Japanese patients with type 2 diabetes mellitus. Compared with male extensive metabolizers, female intermediate metabolizers [adjusted odds ratio (OR), 2.43; 95% confidence interval (95% CI), 1.17-5.06] and poor metabolizers (OR, 7.49; 95% CI, 2.64-21.26) were at a significantly higher risk of developing DR. Furthermore, the CYP2C19 poor metabolizer genotype was found to be an independent risk factor for DR only in women when patients were stratified by sex (OR, 4.18; 95% CI, 1.42-12.26). This is the first report showing the interactive effect of sex and CYP2C19 polymorphisms on microvascular disease in humans, although further investigations are needed to verify these findings.