BACKGROUND: This study aimed to clarify whether children with neurocardiogenic syncope (NCS) differ from healthy control subjects in baseline heart rate variability (HRV) and in their response to orthostatic stress induced by active standing and tilt table. METHODS: This study analyzed the difference between 55 children with a history of NCS or presyncopal symptoms (PS) and healthy control subjects. Measurements included short-term HRV during resting position, tilt table testing, and active standing. Time and frequency domain HRV parameters were computed. RESULTS: Both the NCS and PS children differed significantly from healthy control subjects during resting position. During tilt table testing, nearly all NCS and PS subjects differed significantly from the control group in calculated HRV parameters. Moreover, for the low-frequency power and total power, the confidence intervals did not overlap. CONCLUSIONS: The findings suggest that chronic autonomic differences exist between healthy children and patients with NCS and PS. These changes could be detected even by short-term HRV recordings. The tilt table maneuver provoked the most prominent differences between the groups. Low-frequency power and total power during tilt table testing helps to detect children with NCS.