Ob jective To research the gene expression profile of aura-absence migraine patients before and after acupuncture of Shaoyang meridian acupoints or non-acupoints. Methods Twenty aura-absence migraine patients were randomly divided into meridian acupoint group and non-acupoint group, 10 cases in each group. Gene chip technology was used to investigate the differences of two sets of gene expression profiles, and reverse transcription-polymerase chain reaction (RT-PCR) was applied for the analysis of partial genes to verify the accuracy of gene chip detection results. Results Seventy-two differentially expressed genes were obtained in meridian acupoint group, and 110 differentially expressed genes were obtained in non-acupoint group. The function genes of meridian acupoint group involved brain endorphin enzyme, adenosine triphosphate ( ATP) synthase, etc., which were closely related with the curing of aura-absence migraine. Non-acupoint group had extensive and scattered function genes involving apoptosis, DNA repair, etc., which had less correlation with the curing of aura-absence migraine. ATPAF2, PTGS2, TOR3A genes of meridian acupoint group and ACP2, AURKA, ARHGEF11, CASP8 gene of non-acupoint group presented by RT-PCR analysis had verified the reliability of microarray data. Conclusion The therapeutic effect of meridian acupoints acupuncture for aura-absence migraine has achieved through the multi-gene action at the molecular level, but the corresponding target genes for the placebo effect of non-acupoint acupuncture have not been found , which demonstrates the existence of meridian effect.