Magnetic resonance imaging (MRI) studies occasionally display focal hyperintense lesions within the white matter of migraine patients. No immunological factors associated with these lesions have been defined so far. To investigate the relationship between MRI lesions and antineuronal antibody response, 17 migraine patients with white matter lesions (WML), 19 migraine patients without WML, 20 multiple sclerosis patients with WML and with no headache history, and 20 healthy individuals were enrolled, and their sera were examined by indirect immunohistochemistry for the presence of immunoglobulin G (IgG) reacting with the rat brain tissue. Migraine patients with and without WML essentially showed identical demographic and clinical features and frequencies of systemic autoantibodies. However, migraine patients with WML displayed a significantly higher frequency of antineuronal antibodies than those without WML (12/17 vs. 2/19, p = .0004). Serum IgG of migraine patients predominantly reacted with the cytoplasm of neurons and the molecular layer of cerebellum. None of the multiple sclerosis patients and healthy controls displayed antineuronal antibodies. Our results imply the involvement of inflammation in migraine pathogenesis.