Acute ethanol consumption affects the CNS. However, each role of brain cells in ethanol-induced brain action has been clarified. In the present study, we estimated the differences in mRNA expression of innate immune system- and ion channel-related genes among the rat brain slices and primary cultures of astrocytes, microglia or neuron from the rat to evaluate each role of brain cells in ethanol-induced brain damage. Organotypic brain slice cultures were performed to examine various genes expression with or without 50-mM ethanol treatment. Male Wistar rats (8 weeks old) were carbon dioxide-anesthetized and quickly decapitated. After dissection of the brain and removal of the frontal and occipital poles (including the cerebellum), the specimens were sliced into 200 µm thick sections on a LEICA VT1000S tissue slicer and cultured in a CO2 incubator. Three hours later, the slice was incubated in the medium with or without 50-mM ethanol for 12 hours. Thereafter, the expression of various mRNAs in the specimens was detected by a quantitative real-time RT-PCR system. On the other hand, Neurons and glial cells were isolated from the hippocampus of E18-19 rat embryos and the forebrain of newborn rats, respectively. After ethanol treatmen, the cells were isolated and lysed in the lysis buffer. The mRNA expression was performed by qRT-PCR. Ethanol treatment significantly increased the expression of oxidative stress-, ion channel- and glutamate receptor-related genes compared as non-treatment with ethanol in the organotypic brain slice which consists of neurons, astrocytes, microglial cells, NG2 glial cells, oligodendrocytes and so on. The differences in the ethanol-induced expression of mRNA among these cells could be found. Innate immune system-related gene expression was significantly increased in the slice and microglial cells compared as other cells. On the other hand, the potassium channel-related gene expression was significantly increased in the slice and astrocyte. Therefore, these findings suggested differential role of brain cells in ethanol-induced mRNA expression.