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The present study was designed to determine microtubule-associated protein-2 and synaptophysin expression in the hippocampal CA3 region in a rat model of middle cerebral artery occlusion. The rats were treated with acupuncture at Baihui (GV 20), Qubin (GB 7), and Qianding (GV 21) points, in addition to exercise training. Results were compared with rats undergoing exercise training only. The Y-maze method and immunohistochemistry revealed decreased error frequency of passing through Y-maze, as well as significantly increased microtubule-associated protein-2 and synaptophysin expression, in the acupuncture with exercise training group compared with the model and exercise training groups after 5 weeks. Microtubule-associated protein-2 and synaptophysin expressions negatively correlated with error frequency of passing through the Y-maze. These results suggested that acupuncture combined with exercise training improved learning and memory functions in a rat model of cerebral infarction. The mechanisms of action were hypothesized to be associated with dendritic or synaptic plasticity in the ipsilateral hippocampal CA3 region.