Background Autonomic nervous system (ANS) symptoms are frequently present in people with epilepsy (PwE). They are generally more prominent when they originate from the temporal lobe. We aim to investigate the alterations of autonomic functions during the interictal period in patient with temporal lobe epilepsy (TLE) and idiopathic generalized epilepsy (IGE) using heart-based tests, blood pressure (BP)-based tests and sympathetic skin response (SSR). Forty-eight PwE with disease duration ranging from 2 to 15 years and 51 healthy individuals were studied. Long-term electroencephalography (EEG) monitoring, the heart rate variability (HRV) during normal breathing, deep breathing, Valsalva maneuver and standing, BP responses during standing, to isometric hand grip and to mental arithmetic, and the SSR was recorded for all participants. Results 31 patients with TLE and 17 with IGE showed lower RR-IV values during deep breathing, Valsalva maneuver and standing, but not during rest, impaired BP responses during standing, isometric hand grip, and mental arithmetic. Also, prolonged SSR latencies. Within PwE group, no difference was noticed between males and females, nor between the left and right temporal lobes. Conclusion Abnormal autonomic (sympathetic and parasympathetic) regulatory functions suggest that epilepsy may alter the autonomic function and this is not only in TLE but rather in IGE too. These autonomic changes are irrespective of the localization of epilepsy between the two hemispheres. The ANS changes in epileptic patients, particularly those with autonomic symptoms, confirm that electrophysiologic measures of autonomic function may be of value in preventing sudden unexpected death in epilepsy.