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Purpose: The objective of this study is to investigate alteration of autonomic nervous system (ANS) activity in patients suffering from erectile dysfunction (ED) by comparing parameters of heart rate variability (HRV) between men with ED and healthy subjects. Methods: A retrospective review was performed on 40 ED patients (mean age, 46.0±8.49 years) without any disease and 180 healthy control people (mean age, 44.4±7.83 years) without ED in our institution from June 2008 to July 2010. And electrocardiographic signals were obtained to measure HRV parameters for both patients and controls in a resting state. Results: For the time domain analysis, square root of the mean differences between successive RR intervals (RMSSD) representing parasympathetic activity was lower in patients than controls although P-value was not statistically significant (P=0.060). For the frequency domain analysis, high frequency (HF) representing parasympathetic activity was lower in patients than controls (P=0.232) and low frequency (LF) representing mainly sympathetic activity was higher in patients than controls (P=0.416). Lastly, LF/HF ratio reflecting sympathetic/parasympathetic activity ratio was statistically higher in patients than controls (P=0.027). Conclusions: Patients with ED exhibited different HRV parameters compared with normal controls. This suggests that the patients with ED may have some kind of imbalance in the ANS and it may be possible that general imbalance of the ANS is one of the causes of ED. Thus, HRV analysis may give valuable diagnostic information and serve as a rapid screening tool to evaluate altered ANS activity in patients with ED.