OBJECTIVE: To compare the effects of electroacupuncture (EA) of different acupoint groups on heart rate variability (HRV) and cerebral glutamate (Glu) and aspartic acid (Asp) contents in cerebrocardiac syndrome (CCS) rats. METHODS: A total of 52 Wistar rats were randomized into normal (n = 8), sham-operation (sham, n = 8), model (n = 12), Shuigou-Fengfu (GV 26-GV 16, n = 12), and Neiguan-Xinshu (PC 6-BL 15, n = 12) groups. CCS model was established by intracerebral (Caudate nucleus) injection of clostridiopeptidase (1 U/microl) plus heparin (7 U/microl). EA (2 Hz/100 Hz, 1-3 mA) was applied to GV 26-GV 16 and PC 6-BL 15 for 20 min, once daily for 3 days. Cerebral Glu and Asp contents were detected by high performance liquid chromatography, and HRV was analyzed by SMUP Software. RESULTS: In comparison with normal and sham groups, the R-R interval (RRI) of electrocardiogram and total variability (TV) of HRV, cerebral Glu and Asp contents in model group increased significantly (P < 0.01, P < 0.05), and the ratio of low frequency/high frequency (LF/HF) decreased evidently (P < 0.01). Compared with model group, RRI and TV values, and cerebral Glu and Asp contents of EA of GV 26-GV 16 and PC 6-BL 15 groups reduced markedly (P < 0.01, P < 0.05), LF/HF of the later two groups increased evidently (P < 0.01). No significant differences were found between GV 26-GV 16 and PC 6-BL 15 groups in RRI, TV and LF/HF of HRV, and cerebral Glu and Asp contents (P > 0.05). CONCLUSION: EA of both GV 26-GV 16 and PC 6-BL 15 can effectively improve CCS in rats, which is closely associated with their effects in lowering cerebral Glu and Asp levels and in suppressing the excitability of sympathetic nerve.