The clinical symptoms of migraine point to autonomic disturbances, especially to disrupted regulation of the circulatory system and autonomic balance. Searching for more accurate autonomic system studies we turned to the spectral analysis of cardiac rhythm changes, that allows to estimate the autonomic balance in sinus node. 44 patients with migraine were studied and the results were compared with those obtained in 74 healthy subjects. The reduced influence of both sympathetic and parasympathetic part of autonomic system on the sinus rhythm in migraine patients was found. The autonomic balance is shifted to the parasympathetic innervation side in patients with migraine.