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鈥?/-鈥?.2鈥痽ears old) who presented with NMS and 20 healthy individuals (age 26.6鈥?/-鈥?.7鈥痽ears old) who served as controls. HRV was measured in supine, sitting and standing positions. Heart rate (HR), low frequency (LF 0.04-0.15鈥疕z), high frequency (HF鈥?鈥?.15鈥疕z), 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鈥?鈥?.05). HR was higher in all positions in patients with NMS than in healthy individuals (p鈥?鈥?.05). CVRR in the supine position was lower in the patients with NMS (p鈥?鈥?.001), and it was significantly lower in patients who were positive in an orthostatic test (p鈥?鈥?.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%. CONCLUSION: 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.