BACKGROUND: Dysfunction of the autonomous nervous system causes arrhythmias and, although previous studies have investigated the effects of epilepsy on the autonomic control of the heart, there is still uncertainty about whether imbalance of sympathetic, vagal, or both systems occurs in epilepsy as well as the effect of anticonvulsants on the autonomic system. AIM: To evaluate cardiac autonomic status in children with epilepsy on antiepileptic drugs. PATIENTS AND METHODS: Sixty patients with epilepsy were recruited from the Outpatient Neurology Clinic at Ain Shams University and were divided into the following groups: group I, drug naive; and group II, patients with epilepsy on regular antiepileptic drugs. The second group was further subdivided into the following groups: group Ha, received monotherapy; and group lib, received polytherapy. Forty age- and sex-matched healthy children served as controls. Included patients underwent videorecorded electroencephalograph, Holter electrocardiogram (ERG) for time and frequency domains of heart rate variability, and standard ERG recording for QTc, QTd. RESULTS: Mean values of all time domain, total power, and high-frequency power were significantly lower, whereas low-frequency and low-frequency/high-frequency power, QTc. and QTd were significantly higher in group I compared with group II and in patients compared with controls. No significant difference was found between patients on different antiepileptic drug regimens regarding heart rate variability values. A significant negative correlation was found between Chalfont severity score and 50% of difference between adjacent, normal RR intervals in patient groups. CONCLUSIONS: Children with epilepsy have cardiac autonomic dysfunction evident in their heart rate variability assessment. Patients on antiepileptic drugs had better autonomic balance than those not on antiepileptic drugs. Holter and ERG follow-up should be considered for early detection in those at high-risk cardiac complications.