ABSTRACT: Glaucoma is the leading cause of irreversible blindness and the second most common cause of all blindness after cataracts. This study investigates the association of polymorphism in the CYP46A1 and PPAR?2 genes and primary open angle glaucoma (POAG).This study evaluated 122 POAG cases (POAG group) and 112 cases of nonglaucomatous patients (control group). Polymorphisms of the CYP46A1 gene and PPAR?2 gene were evaluated with the polymerase chain reaction-restriction fragment length polymorphism method in both groups.The mean ages were 49.88 ± 12.34 years and 53.74 ± 11.87 years for the POAG group and control group, respectively. The CYP46A1 gene CC, CT, TT genotype frequencies were 13.93%, 58.2%, 27.87% in the POAG group and 19.6%, 40.19%, 40.19% in the control group, respectively. The PPAR?2 gene CC, CG, GG genotype frequencies were 16.83%, 54.45%, 28.71% in cases and 3.92%, 28.43%, 67.64% in the control group, respectively. Statistically, significant differences in the frequencies of CYP46A1 CC, CT, TT and PPAR?2 CC, CG, GG (P < 0.05) genotype were found between groups (P < 0.05, all comparisons).Findings of this study suggest that CYP46A1 gene and PPAR?2 gene polymorphisms can be a predictive marker for early identification of population at risk of POAG, although a larger sample size is required to determine the role of these polymorphisms in the pathogenesis and course of POAG.