Purpose: Heart rate variability (HRV) is a tool used to measure autonomic nervous function; however, there is no evidence that it can be used to define sympathetic hyperactivity in men with lower urinary tract symptoms (LUTS). We suspected that LUTS would differ between sympathetic hyperactive and hypoactive patients. Therefore, we measured HRV and divided the LUTS patients into two groups, a sympathetic hyperactive group and a sympathetic hypoactive group according to the low frequency/high frequency (LF/HF) ratio and made clinical comparisons between the groups. Methods: A total of 43 patients with symptomatic LUTS (International Prostate Symptom Score [IPSS] over 8) and 49 healthy volunteers were enrolled. No subjects had diseases that could affect the autonomic nervous system, such as diabetes or hypertension. Electrocardiographic signals were obtained from subjects in the resting state and HRV indexes were calculated with spectral analyses. We divided the LUTS patients into two groups by an LF/HF ratio of 1.9, which was the median value in the healthy volunteers, and compared the differences in clinical characteristics, IPSS, prostate-specific antigen (PSA), and transrectal ultrasound (TRUS) results. The parameters were compared by independent sample t-test by use of SPSS ver. 19. Results: There were no significant differences in age, serum PSA, or volume of the prostate between the 2 LUTS groups. However, analyzing IPSS questionnaires between two groups showed that there were significant differences in mean of Q2 score (frequency) and storage symptom score ([Q2+Q4+Q7]/3) (P<0.05). Conclusions: We suggest that an imbalance of autonomic nervous system activity may be a factor that evokes varieties of symptoms in men with LUTS. LUTS patients with hypoactive sympathetic tone may suffer from frequency and storage symptoms.