BACKGROUND: Synapses undergo high levels of plasticity within the nervous system, and cerebral ischemia induces synaptic plasticity changes. OBJECTIVE: To demonstrate the effects of electroacupuncture on ultrastructural synaptic changes in the focal cerebral ischemia marginal zone in rats using quantitative analysis of stereological measurement. DESIGN, TIME AND SETTING: A randomized, controlled, animal experiment was performed at the Experimental Animal Center and Laboratory of Electron Microscopy, Guangzhou University of Traditional Chinese Medicine from January 2008 to January 2009. MATERIALS: The G-6805 electric acupuncture apparatus was provided by Shanghai Huayi Instrument Factory, China. METHODS: A total of 90 male, Wistar rats were randomly assigned to sham-surgery, model, and electroacupuncture groups, with 30 animals in each group. Each group was subdivided into 1 hour, as well as 1, 3, 7, and 21 days post-surgery groups, with six animals assigned to each time point. Heat coagulation-induced occlusion of the middle cerebral artery was performed to establish a model of focal cerebral ischemia. Electroacupuncture was applied immediately following surgery to the electroacupuncture group [4/20 Hz, 2.0-3.0 V, 1-3 mA, to Baihui (GV 20) and Dazhui (GV 14)] for 30 minutes. Treatment was performed once a day, and experimental animals were sacrificed, at 1 hour, as well as 1, 3, 7 and 21 days post-surgery. MAIN OUTCOME MEASURES: At different time points after intervention, changes in synaptic ultrastructure, such as postsynaptic density thickness, synaptic cleft width, and synaptic interface curvature, were observed in the focal cerebral ischemia marginal zone in rats through the use of transmission electronic microscopy. RESULTS: Broken synapses were observed following cerebral ischemia, and the number of synapses was significantly decreased. Compared to the model group, synaptic ultrastructure was significantly improved in the electroacupuncture group. Compared to the sham-surgery group, postsynaptic density thickness was significantly decreased, as were synaptic cleft width and synaptic interface curvature in the electroacupuncture and model groups. However, compared to the model group, postsynaptic density thickness was significantly increased in the electroacupuncture group at the same time point post-surgery (P < 0.05 or P < 0.01). In addition, synaptic cleft width and synaptic interface curvature were significantly increased with the passage of time (P < 0.05 or P < 0.01). CONCLUSION: Electroacupuncture significantly ameliorated structural synapse lesion during the early stage of cerebral ischemic injury, promoted repair of synaptic structure, improved structural parameters of synapses, and increased synaptic structural plasticity, which suggested that the therapeutic effect of electroacupuncture was related to synaptic reorganization.