Obesity is the major risk factor of the heart disease and the metabolic disease. The autonomic nervous system is a key contributor in the regulation of energy balance, so the blunted activity may contribute to the maintenance of the obese state. So we evaluated the function of the autonomic nervous system in young overweight and obese women with heart rate variability. Methods The subjects were 26 overweight and obese young women(BMI〉23㎏/㎡) and 25 lean women who visited Kangnam Kyunghee hospital for obesity management from March 2006 to April 2008. Bioimpedance Analysis (BIA), short-term spectral analysis of heart rate variability (HRV) were performed. Results HRV of obese young group was lower than the lean young group, but there is no statistical significance. BMI had significantly a negative correlation with Low Frequency(LF) of HRV. LF power is mediated by sympathetic nervous system activity. These results indicate a decrease of sympathetic modulation in overweight and obese young women. Conclusions Overweight and obese young women have decreased sympathetic nervous system activity. In clinical practice, an assessement of HRV would be noninvasive and sensitive methods for sympathetic nervous system of young overweight and obese women.