The effect of the epiphysis hormone melatonin on the brain bioelectrical activity is understudied: the data of experimental and clinical studies of melatonin effects are inconclusive and related mostly to exogenous administration. We studied 43 patients with focal epilepsy, 25 patients with cryptogenic epilepsy and 18 with symptomatic epilepsy. Carbamazepine and valproate were used as anticonvulsive drugs. Morning and evening urine concentrations of 6-sulfatoxymelatonin (6-COM), the main melatonin metabolite, were determined twice using immunoassay method: in autumn at the inclusion in the study and beginning of the anticonvulsant treatment and after 6 months, in spring, when anticonvulsant doses had been adjusted. The presence of epileptic seizures was associated with the reduction of melatonin concentration in the body that was supported by the decrease of urine 6-COM, in particular in the morning, in non-treated patients. Prescription of anticonvulsant treatment resulted in the increase of 6-COM. The concentration of the morning urine 6-COM was higher in patients with focal epilepsy receiving anticonvulsant treatment with valproate compared to those receiving carbamazepine: 49.28±6.71 and 37.09±5.43 ng/ml versus 20.00±3.6 and 13.11±2.08 ng/ml in patients treated with valproate and carbamazepine, respectively, before and after the adjustment.