Autonomic nervous system involvement in subacute sclerosing panencephalitis was studied in 29 patients by analysis of heart rate variability and compared with a control group which consisted of 20 age- and sex-matched healthy subjects. Holter recordings for 24 hours were obtained, and all recordings were analyzed using time-domain parameters. The patients with subacute sclerosing panencephalitis were found to have significantly lower values of standard deviation of all normal sinus intervals and triangular index when compared with the control group. Of 23 patients who had regular follow-up, 15 died in a period ranging from 1 to 13 months. Twelve of these patients had heart rate variability parameters lower than normal, but no significant difference was observed between the heart rate variability values of patients who survived or died. Also, there was no association between brain magnetic resonance imaging findings and heart rate variability indices. It is concluded that patients with subacute sclerosing panencephalitis have autonomic dysfunction; and this was thought to be mainly due to central involvement.