Objective To observe the effect of basal nuclei lesion on the choline acetyltransferase (ChAT) and synaptophysin in rats brain Methods The Ibotenic acid was injected into the bilateral nucleus basalis of Wistar rats to make the model of Alzheimer disease (AD) The changes of learning and memory were observed with water maze and the expressions of ChAT and synaptophysin in brain were measured with in situ hybridization, immunohistochemistry and image analysis Results The ability of learning and memory, the contents of ChAT and synaptophysin in the groups with the lesion of cholinergic system decreased significantly compared with shame operation group and control group Conclusions Protecting central and increasing the level of synaptophysin could improve the ability of learning and memory