The purpose of this study was to examine the effects of different exercise intensities with the anaerobic threshold (AT) as the standard on electroencephalograph (EEG) and heart rate variability (HRV). Eleven healthy males, with a mean age of 22 (SD 1.48) years, performed submaximal exercise to determine their ATs, and underwent four experimental conditions including rest (rest), 20% less than the AT level (-20), the AT level (AT), and 20% more than the AT level (+20) for about 20 minutes. EEG and electrocardiogram (ECG) were taken for 15 minutes before and after each experimental condition, respectively. The EEG signals were recorded from Cz, Pz, O1 and O2 (10-20 system). HRV was determined by the R-R interval method of ECG. Spectral analysis was applied to the EEG and the HRV from just before (pre) and after (post) each experimental condition for 5 minutes using the maximum entropy method (MEM). Post/pre ratios were calculated, after the power spectral density (PSD) and percentage of total power (power time percent: Time%) of delta (0.5-4 Hz), theta (4-8 Hz), alpha 1 (8-11 Hz), alpha 2 (11-14 Hz), beta 1 (14-20 Hz), beta 2 (20-30 Hz), total waves in EEG and PSD as to low frequency (LF: 0.04-0.15 Hz) and high frequency (HF: 0.15-0.4 Hz) areas, and the LF/HF(L/H) ratio in HRV were analyzed. In the exercise condition, total PSD in the EEG was enhanced and PSD of HF in HRV was significantly declined, as compared to those in the resting condition. Alpha PSDs of occipital sites were higher in -20 than those in AT and +20 conditions. The increase in L/H in AT and +20 demonstrated the changes in the balance of the autonomic nervous system, compared with that in -20. A significant increase in heart rate was observed in +20, although other indicators did not show differences in AT and +20 conditions. No alternations were noted in the gradient of exponential PSD in the above four experimental conditions, that is at rest, -20, AT and +20. These results suggest that the exercise intensity 20% less than one's AT level does not put a great strain on his or her body in health-promoting.