Objective. To study circadian regulation of a cardiac rhythm and functionality of the heart. Methods. An experimental study was carried out in rats WAG/Rij with a genetically determined absence epilepsy. Results. The maximum number of spike-wave discharges (SWD) occurred at night, early in the morning and evening, and the minimum number was observed from 8 a.m. to 16 p.m. The night functional capabilities of heart were reduced. Conclusions. The decrease in the number of SWD and spike-wave index in the daytime contributes to the realization of opportunities of the central mechanisms of autonomic regulation of the heart. At night, when the seizure activity is increased, these opportunities are limited.