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Melatonin is a potent antioxidant agent that can scavenge oxy- and nitroradicals generated under hypoxic conditions in the brain. In this study, we investigated the effect of melatonin on protein oxidation and nitric oxide (NO) during hypoxia. Seven-day-old Sprague-Dawley newborn rats were divided into three groups. Hypoxic (n=9) and melatonin (n=11) groups were subjected to 2h of hypoxic exposure (a humidity mixture of gases consisting of 92% nitrogen and 8% oxygen). Melatonin (at a dose of 10mg/kg) was administrated 30 min before the onset hypoxia and then at 24th and 48th hours after the end of the hypoxic exposure. Control (n=10) and hypoxic groups received the isotonic sodium chloride according to the same schedule. The brain tissue concentration of advanced oxidation protein products (AOPP) and protein thiol (P-SH) was used as an index of protein oxidation. In our study, although AOPP and NO increased significantly, the levels of P-SH decreased in the hypoxic group. The level of AOPP was declined by melatonin treatment. However, perturbed thiol status could not be recovered by melatonin treatment. There was no relationship between the levels of NO and protein oxidation markers. These results indicate that exogenous melatonin could prevent AOPP, but that it is inadequate in recovering perturbed thiol status. Therefore, melatonin alone was observed to be an incomplete treatment to prevent protein oxidation in hypoxia-induced brain damage.