BACKGROUND The effectiveness of using acupuncture to treat migraine is rarely and even suspectedly reported in the literature. In this article, we report the design and the protocol of a randomized controlled large-scale trial to treat migraine using acupuncture, aiming at testifying it is effective to use acupuncture to treat migraine. We demonstrate also that the effectiveness of the treatment may vary due to using acupoints of different meridians or different acupoints of one meridian. METHODS A multi-center randomized controlled trial is currently undergoing, with three acupoints treatment groups and one non-acupoints control group. The acupuncture treatment consists of 20 sessions per patient with a observation period of 20 weeks. In total, 480 patients with migraine are registered in this study within 8 hospitals in China from March 2008 to June 2009. These patients are randomly assigned to receive one of the following four acupoints treatment groups, i.e. 1) specific acupoints of Shaoyang meridians (120 patients), 2) non-specific acupoints of Shaoyang meridians (120 patients), 3) acupoints of other meridians (120 patients); or 4) non-acupoints control group (120 patients). The main outcome measurement in this trial is the effect comparison achieved among these four groups in terms of number of days with migraine and intensity of migraine during and after the baseline phase, i.e. the first 4 weeks before randomization and 4, 8 and 16 weeks after randomization. The intensity of headache including headache intensity grade (0-3) and visual analogue scale (VAS) score will also be used in this study. In addition, the differences of Migraine-Specific Quality-of-Life Questionnaire (MSQ) and Transcranial Doppler Sonography (TCD) before and after randomization are also used as the secondary outcome measurement. CONCLUSIONS The result of this trial (which will be available in 2009) will demonstrate the efficacy of using acupuncture to treat migraine, and verify whether the specific effect of acupoints exists and whether this specific effect of acupoints is related to meridian and a collection of meridian Qi. BACKGROUND Clinical Trials.gov NCT00599586.