Abstract The diagnosis of migraine can sometimes be difficult because some patients do not fulfill the International Headache Society's criteria for migraine. Hence, an accurate and reliable diagnostic marker for migraine is required. In this study, lymphocytes were used to establish Epstein-Barr virus (EBV)-immortalized lymphoblast cell lines, which were then analyzed using a differential cRNA microarray analysis. The gene expression results were validated using real-time polymerase chain reaction. Gene expression profiling identified 15 genes as being differentially expressed in lymphoblasts originating from patients diagnosed as having migraine with aura (MA). One-fifth of these genes were associated with cytoskeletal proteins. The expressions of seven genes increased significantly by more than 50% of the value in the controls, while the expressions of eight genes decreased significantly by more than 50% of the value in the controls. We also verified that the expression of α-fodrin, which was 1 of the 15 genes that were differentially expressed in lymphoblasts originating from patients with MA, increased after cortical spreading depression in an animal model. Thus, α-fodrin might play an important role in the pathophysiology of migraine, possibly serving as a migraine biomarker.