Background The mechanism of acupuncture analgesia in craniotomy has been widely studied.However,the theoretical basis for selection of acupoints has not been examined.In this study,we used the regional homogeneity method blood oxygen level-dependent (BOLD) signals to determine changes in brain activity in response to transcutaneous electrical stimulation on acupoints and non-acupoints in resting state functional magnetic resonance imaging (fMRI).Methods Twelve healthy volunteers were enrolled in this study.BOLD fMRI scanning of the brain was performed for 306 seconds before and 30 minutes after transcutaneous electrical stimulation on acupoints UB63 (Jinmen),LV3 (Tai chong),ST36 (Zusanli),and GB40 (Qiuxu).The procedure was repeated after one week with stimulation on non-acupoints (one was 9 above BL67,the second was 12 above BL67 (Kunlun),the third was 7 above Kl3,and the fourth was 10 above Kl3 (Taixi)).Results The regional homogeneity in the acupoint group was increased in the left thalamus,caudate,putamen,lentiform nucleus (BA19,30,39),postcentral gyrus,precentral gyrus (BA3,4,30,32),calcarine fissure,middle temporal gyrus (BA30),right superior temporal gyrus,inferior temporal gyrus (BA38),cuneus,and precuneus (BA7,19) when compared to the non-acupoint group.The regional homogeneity of the acupoint group was decreased in the left cerebellum posterior lobe,middle frontal gyrus (BA10),double-side precuneus (BA7),and the postcentral gyrus (BA40).Conclusions The brain region activated following acupoint stimulation is the ipsilateral pain-related brain region,which may relate to the therapeutic effect of acupuncture on pain relief.Further acupoint stimulation causes different central nervous responses compared to non-acupoint stimulation.