Objectives : The authors tried to investigate the characteristics of Heart Rate Variability(HRV) among the subjects with metabolic syndrome for testing the possibility of clinical application of HRV in evaluating metabolic syndrome. Methods : We examined the difference of the means of HRV between 122 subjects of metabolic syndrome and 1057 healthy controls using T-test, and the change of means in HRV according to increasing risk factors of metabolic syndrome. Using multiple regression analysis, we examined the association of HRV with the risk factors of metabolic syndrome. Results : The HRV indices including SDNN(Standard Deviation of all normal NN intervals), RMSSD(the square Root of the Mean Squared Differences of successive all normal NN interval), TP(Total Power), LF(Low Freuency), and HF(High Frequency) were significantly lower in the metabolic syndrome group than in the normal control group, and the means of all HRV indices except LF/HF were decreased consistently according to increasing risk factors of metabolic syndrome. The fasting glucose, triglyceride, and waist circumference were dependent factors that contributed significantly to the change of HRV. Conclusion : These findings suggest metabolic syndrome adversely affects cardiac autonomic system and HRV could be a useful method for evaluating metabolic syndrome.