This study was undertaken to investigate the effects of electroacupuncture(EA) on Choksamni(ST36), a well-known acupuncture site, on nicotinamide adenine dinucleotide phosphate-diaphorase(NADPH-d), neuropeptide Y(NPY) and vasoactive intestinal peptide(VIP) in the cerebral cortex of spontaneously hypertensive rats(SHR). EA on Choksamni was applied using 2Hz electrical biphasic pulses of 10min, 3 times a week for a total of 10 sessions. Thereafter we evaluated changes in NADPH-d-positive neurons histochemically and changes in NPY and VIP-positive neurons immunohistochemically. The optical density of NADPH-d-positive neurons in the Choksamni group was significantly lower in all areas of the cerebral cortex than in the control group. However, the optical density of NPY-positive neurons in the Choksamni group was similar to that of the controls in most areas of the cerebral cortex, with the exception of the primary motor and visual cortices. The optical density of VIP-positive neurons in the Choksamni group was significantly decreased as compared to the control group in most areas of the cerebral cortex, with the exception of the cingulate cortex. The present results demonstrated that EA on Choksamni changes the activity of the NO system, and that stimulation at the same level, causes selective changes within the peptidergic system in the cerebral cortex of SHR.