Abnormal electroencephalography (EEG) in migraineurs has been reported in several studies. However, few have evaluated EEG findings in migraineurs during a time period when neither the last attack nor the next attack may interact with the results. We, therefore, compared interictal EEG in migraineurs and headache-free subjects with a design controlled for interference by pre-ictal changes. Pre-ictal EEG findings in the painful cranial side during the next attack after registration were also investigated. Correlations between clinical variables and EEG are reported as well. Interictal EEGs from 33 migraineurs (6 with and 27 without aura) and 31 controls were compared. Absolute power, asymmetry and relative power were studied for delta, theta and alpha frequency bands in parieto-occipital, temporal and fronto-central areas. EEG variables were correlated to attack frequency, headache duration, attack duration, pain intensity, photo- and phonophobia. Compared with controls, migraineurs had increased relative theta power in all cortical regions and increased delta activity in the painful fronto-central region. Absolute power and asymmetry were similar among groups. In age-adjusted analyses, headache intensity correlated with increased delta activity. In this blinded controlled study, we found globally increased relative theta activity in migraineurs. A slight interictal brain dysfunction is probably present between attacks.