We always diagnose migraine using the International Classification of Headache Disorders criteria (version 3). However, since this criteria depends on clinical symptoms and the pathophysiology of migraine is not fully understood, diagnosis sometimes differs between doctors. Hence, we investigate for an appropriate diagnostic biomarker of migraine using the omics approach—a comprehensive analysis of transcriptome, proteome, and genome. Dysfunctions of α-fodrin, apolipoprotein E, and GC-binding protein were found to be candidate biomarkers through proteome, transcriptome, and genome analyses, respectively. Although currently we cannot narrow down to one candidate biomarker, this can be subsequently achieved by evaluating a larger number of patients.