In this study we investigated whether pretreatment with melatonin was protective against the injury of the central nervous system(CNS) in rats receiving LD50 whole body irradiation. The wistar rats were randomized into four groups: i) the control group(CG), ii) melatonin-administered group(MG; 1 mg/kg body weight), iii) irradiated group (RG; 6.75 Gy, one dose), and iv) melatonin-administered and irradiated group (MRG). Blood samples were drawn from the rats 24 h after the treatment and plasma glutathione levels were assayed. Plasma glutathione level was significantly higher in RG than CG. The melatonin pretreatment prevented GSH increase induced by irradiation. Lipid peroxidation and glutathione levels of rat cerebral cortex were determined in all groups after 24 h. Cortical malondialdehyde (MDA) was significantly higher in the RG. The melatonin pretreatment prevented cortical MDA increase induced by irradiation. Cortical GSH was significantly lower in RG than the CG. The melatonin pretreatment prevented cortical GSH decrease induced by irradiation. Tissue samples were obtained from cerebral cortex and hypothalamus which also were affected by ionizing irradiation in the CNS and were evaluated with electron microscopy. Histopathological findings showed that LD50 whole body irradiation resulted in damage of the neuronal cells of CNS. The results obtained from this study demonstrated that pretreatment with melatonin prevented the damage that develops in CNS following irradiation. The beneficial effect of melatonin can be related to protection of the CNS from oxidative injury and preventing the decrease in the level of cortical glutathione.