In this study, effect of whole body ionizing irradiation on pineal gland in rats and possible protective effects of melatonin (MLT) were investigated by chronobiological and electron microscopic methods. For this purpose 48 male Wistar rats consisting of 6 group that were; control (morning and evening groups), whole body irradiation (WBI) (morning and evening groups), whole-body irradiation+melatonin (WBI + MLT) (morning and evening groups) were used. WBI group exposed to sublethal (below the lethal dose) irradiation dose of 8 Gy using 60Co source (Chisostat therapeutic device, revealing rate 0.29 Gy.dak-1) focusing of 80 cm away from the skin in morning (09.00 am) and evening (09.00 pm). Melatonin administered intraperitoneally immediately before (10 mg/kg), after (20 mg/kg) and 24 h after (10 mg/kg) whole body irradiated rats. Ultrastructurally, mitochondria and pinealocyte diameters measured and organelle properties were evaluated histologically. Evening groups were the most affected groups by application of irradiation. However, melatonin administration considerably inhibited these degenerative changes. Although there was not any significant differences between two melatonin groups, WBI + MLT morning group was better than that of evening group. We thought that, although in different organelles, rat pineal gland was more sensitive to irradiation in evening than morning. However, we did not find any significant difference between therapeutic effect of MLT administration in morning and evening groups.