Objective To investigate the mechanism of effect of microwave irradiation on central nervous system. Methods The cell membrane Ca 2+ ,Mg 2+ ATPass activities of cerebral cortex,hippocampus,thalamus of Kunming mice exposed to 1 mW/cm 2,5 mW/cm 2,10 mW/cm 2 microwave irradiation were measured by histochemical method. Results In rats underwent 1 mW/cm 2 exposure,the activities of Ca 2+ ,Mg 2+ ATPase of cerebral cortex,hippocampus,as wall as thalamus increased significantly ( P 0.05) as compared with controls .In rats underwent 5 mW/cm 2 exposure,Ca 2+ ,Mg 2+ ATPase of the above 3 parts of brain were not changed obviously,while in 10 mW/cm 2 group, Ca 2+ ,Mg 2+ ATPase activities in cerebral cortex and hippocampus were significantly decreased ,and those of thalamus were not changed significantly. Conclusion Dfferent densities of microwave irradiation may result in diffent reaction of Ca 2+ ,Mg 2+ ATPase of brain. Under 10 mW/cm 2 exposure, negative effect on cerebral cortex and hippocampus came earlier than effect on thalamus. This implies that the learning ability and memory were affected earlier than on thermal regulation under high density microwave irradiation.