Objectives : This study was designed to research whether HRV can yield a suitable diagnosis for activity of autonomic nerve system on functional dyspepsia. Methods : The testing of HRV was carried out at the Oriental Medical Center of Dong-Eui University with the participation of 28 functional dyspepsia patients, 25 dyspepsia caused by organic disease patients and 33 control group people. We checked HRV of the three groups for 5 minutes and compared HRV index(frequency domain analysis: HF, LF, VLF, LF/HF Ratio, TP) between groups. Results were as follows : 1. In the frequency domain analysis, HF, LF, VLF, and TP were significantly lower than the control group in the functional dyspepsia patients and dyspepsia caused by organic disease groups. HF, LF, VLF, LF/HF ratio, and TP were not significantly different between functional dyspepsia group and dyspepsia caused by organic disease group. 2. Age in dyspepsia patient group was significantly higher than in the control group. 3. In the frequency domain analysis, LF, VLF, and TP were significantly lower in the functional dyspepsia group than the control group in age 20-30 years. HF, LF, VLF, LF/HF ratio, and TP were not significantly different between the control group and dyspepsia caused by organic disease group in ages 20-30 years. HF, LF, VLF, LF/HF ratio, and TP were not significantly different between functional dyspepsia group and dyspepsia caused by organic disease group in age 20-30 years. Conclusion : According to this study, autonomic nerve system and parasympathetic nerve system decreased more in the functional dyspepsia patient group compared with the control group.