The pathophysiology of neurocardiogenic syncope (NCS) is only poorly understood. Several studies indicate that NCS is associated with an imbalance of the autonomic nervous system (ANS). We hypothesized that pediatric patients with NCS exhibit alterations of the neurovegetative status also during asymptomatic time periods. To test this hypothesis the non-invasive method of Heart Rate Variability (HRV)-Analysis was used. METHOD: Holter records (12 channel, 180 Hz; obtained during an asymptomatic 24-hour period) of 32 patients (18 male, 14 female, mean age 14.6 yrs) with a history of syncope and a positive Head-Up tilt (HUT) were compared to the recordings of 33 healthy control subjects (19 male, 14 female, mean age 13.5 yrs) with negative history of syncope and HUT. Time domain and frequency domain features were calculated. Analysis segments were divided in different signal duration groups (1, 3, 6, 24 hours). RESULTS: For all time scales the standard deviation of wavelet coefficients yields the best discrimination properties. Analysis of the total time duration (24h) shows only moderate discrimination (sensitivity 84%, specificity 45%) between patient and controls. However, analysis of 3 and 6 hour segments (starting and 6 a.m.) showed significant discrimination: sigma wave scale 13 (6-9 a.m.) sensitivity 78%, specificity 71%., sigma wave scale 11 (6-12 a.m.) sensitivity 84%, specificity 61%. The best combination of two parameters is denoted by SDNN and sigma wave scale 11 (6-12 a.m.) with sensitivity 70%, specificity 75%. CONCLUSION: The results indicate that during an asymptomatic 24-hour-period patients with NCS exhibit an imbalance of the ANS especially in the morning (6-12 a.m.). The findings suggest a time-dependent increased sympathetic or reduced vagal activity in pediatric patients with NCS. Patients could benefit from a time-adjusted medical therapy with beta-blocking agents.