BACKGROUND : Neurally mediated syncope (NMS) is a disorder of autonomic nervous system (ANS) regulation. Orthostatic stress is one of the most common causative factors seen in clinical practice. Analysis of heart rate variability (HRV) is a non-invasive method that is used to assess ANS regulation. In this study, we investigated the pathophysiology of NMS using HRV in our emergency department. METHODS : The subjects were 19 patients (age 25.8 ± 6.2 years old) who presented with NMS and 20 healthy individuals (age 26.6 ± 2.7 years old) who served as controls. HRV was measured in supine, sitting and standing positions. Heart rate (HR), low frequency (LF 0.04-0.15 Hz), high frequency (HF > 0.15 Hz), and coefficient of variation of the R-R interval (CVRR) were determined. RESULTS : LF and HF in the supine position were significantly lower in the patients with NMS (p < 0.05). HR was higher in all positions in patients with NMS than in healthy individuals (p < 0.05). CVRR in the supine position was lower in the patients with NMS (p < 0.001), and it was significantly lower in patients who were positive in an orthostatic test (p = 0.0017). Area under the curve was calculated to be 0.824, and at the cutoff value of 4.997 of CVRR in supine, the sensitivity and the specificity were 78.9% and 85.0%. CONCLUSIONS : The sympathetic and parasympathetic nervous systems were both suppressed in patients with NMS. In post-syncope, parasympathetic withdrawal, rather than sympathetic reactivation, was responsible for the increased HR after syncope. CVRR may serve as a new clinical biomarker in the emergency department.