Genetic factors and the influence of superoxide are known to play roles in the etiology of glaucoma. We evaluated the association between primary open angle glaucoma (POAG) and two polymorphisms in the epithelial nitric oxide synthase (eNOS) gene, and one polymorphism in the myeloperoxidase (MPO) gene. We enrolled 66 patients with POAG and 100 healthy volunteers in this study. The polymorphisms in the eNOS and the polymorphism MPO -463 G-to-A in the MPO gene were resolved by polymorphism polymerase chain reaction (PCR). There were no significant differences in the distribution of the eNOS intron -4 (P=0.481), eNOS promotor -786 (P=0.555), and MPO -463 (P=0.292) gene polymorphisms between the POAG patients and the volunteers (P-values=0.481, 0.555, and 0.292, respectively). None of the alleles from either gene differed between the groups (P-values=0.483, 0.554, and 0.183, respectively). Superoxide is closely related to glaucoma, and eNOS and MPO are two important enzymes in the free radical pathway. However, polymorphisms of the eNOS intron-4, eNOS promotor -786, and MPO -463 gene polymorphisms did not reveal significant differences between POAG patients and controls in our study. The use of these agents and other superoxide-related genes for clinical applications requires further investigation.