BACKGROUND: It is well known that the prone position affects hemodynamics. In this study, we investigate whether the prone position will affect the heart rate variability compared with the supine position. METHODS: Sixty five pediatric patients were assigned to supine group (n = 36) and prone group (n = 29) according to position during surgery. The patients were induced with thiopental and vecuronium and maintained with O2-enflurane-N2O. ECG data was collected for 15 minutes after saturation at the end tidal concentration of the inhalent agent. From the ECG data, power spectral analysis was performed and approximate entropy was calculated. RESULTS: In the prone group, low frequency power and ratio of low to high frequency power were lower and approximate entropy was higher than those in the supine group. Mean heart rate and blood pressure were no different between the two groups. CONCLUSIONS: In the prone position, sympathetic autonomic activity and balance of the autonomic nervous system decreased. However the complexity of regulation of heart rate variability was maintained in the prone position.