Background: The formation of free oxygen radicals has been demonstrated in the corneal tissue after 193 nm laser irradiation. Cornea has several defense mechanisms that protect against oxidative damage. One of them, glutathione peroxidase (GPx), catalyzes the destruction of hydrogen peroxide and lipid hydroperoxide. Selenium is a trace element which is incorporated into the selenoenzyme GPx. In the present study, the effect of excimer laser keratectomy on corneal GPx activities and aqueous humor selenium concentrations in rabbits was evaluated. Methods: Animals were divided into five groups, and all groups were compared: controls (group 1), after epithelial scraping (group 2), transepithelial photorefractive keratectomy (PRK; group 3), superficial traditional PRK (50 pm; group 4) and deep traditional PRK (100 pm; group 5). Corneal GPx activities were measured by a modification of the coupled assay procedure. Aqueous humor selenium concentrations were determined using hydride generation atomic absorption spectrometry. Results: Corneal GPx activities were significantly lower only in group 5 (P<0.05), and the selenium concentration in the aqueous humor did not change in any group. Conclusion: Deep corneal photoablation inhibits GPx enzyme activities in the cornea. Therefore, antioxidants may be useful in reducing free radical-mediated complications after excimer laser corneal photoablation.