The aim of this study was to evaluate possible factors affecting interictal cardiovascular autonomic function in temporal lobe epilepsy with complex partial seizures, paying special attention to hippocampal sclerosis. The study was carried out with 88 patients with epilepsy (22 with left hippocampal sclerosis, 22 with right hippocampal sclerosis, and 44 without hippocampal sclerosis) and 44 healthy subjects. All subjects underwent three tests of cardiac autonomic function: heart rate variation during resting activity, heart rate variation in response to deep breathing and blood pressure response to rising quickly from the supine position. Hippocampal sclerosis and disease duration were found to have significantly important effects on parasympathetic autonomic function, whereas seizure control and type of antiepileptic drug had significant effects on sympathetic autonomic function. This study shows that in addition to factors related to the chronic nature of epilepsy and antiepileptic drug use, hippocampal sclerosis may cause autonomic dysfunction during the interictal period in persons with temporal lobe epilepsy.