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The aim of the present study is to probe candidate genes which were involved in the electro-acupuncture (EA) analgesia and to understand the molecular basis of the individual difference of EA analgesia in rats.EA stimulation at the ST36 acupoints (Zusanli) was applied for 1 h at 1 Hz and nociceptive sensitivity was assessed by recording the tail-flick latency (TFL) induced by radiant heat.Responders and non-responders were determined by Pain Threshold Increase Rate (PTIR) in which the PTIR of responders is more than 30% while the PTIR of non-responders is less than 25% of control.We compared hypothalamus transcriptional profiles of responders with that of non-responders using oligonucleotide microarray.