This study investigates changes in autonomic nervous function through Qi-training. The power spectrum of heart rate variability (HRV) was examined in 20 sedentary healthy subjects and 20 Qi-trainees. It was found that Qi-training in healthy young subjects during controlled respiration increases the high frequency (HF) power and decreases the low frequency/high frequency (LF/HF) power ratio of HRV. These results support the hypothesis that Qi-training increases cardiac parasympathetic tone. In addition, Qi-trainees were found to have higher parasympathetic heart modulation compared with their age-matched, sedentary counterparts. This augmented HRV in Qi-trainees provides further support for long-term Qi-training as a possible non-pharmacological cardio-protective maneuver. In conclusion, Qi-training may stabilize the autonomic nervous system by modulating the parasympathetic nervous system.