Systemically administered kainate has been demonstrated to induce neuronal damage and changes of the levels of biochemical substances related to neurotoxicity. Polyamines are thought to be important in the generation of edema and neuronal cell loss associated with various type of excitotoxicity. Melatonin exerts potent free radical scavenging, antioxidant, and neuroprotective properties. This study was designed to estimate the effect of exogenous melatonin administration on the changes of polyamine levels in rat brains after systemic administration of kainate. Kainate [10 mg/kg, intraperitoneally (i.p.)] was injected into the rats to produce excitotoxicity. Melatonin (15 mg/kg, i.p.) was administered 1 h before, immediately after, and 1 h after kainate treatment. We examined the polyamine [putrescine (PU), spermidine (SD) and spermine (SM)] levels in the cerebral cortex and hippocampus and neuronal density in the hippocampal CA1 and CA3 subsectors in brain sections. PU levels were increased 8 and 24 h after kainate treatment and the administration of melatonin attenuated these changes. Only minor changes were noted in the levels of the polyamine SD and SM after the kainate treatment. In histology, neuronal injuries in the hippocampal CA1 and CA3 subsectors were examined 3 days after kainate treatment and melatonin reduced the kainate-induced neuronal injuries. Our results show that melatonin inhibits the polyamine responses in the cerebral cortex and hippocampus following kainate-induced excitotoxicity and PU may be responsible for the protective effect of melatonin against kainate-induced excitotoxicity.