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Background: Yoga therapy is widely applied to the maintenance of health and to treatment of various illnesses. Previous researches indicate the involvement of autonomic control in its effects, although the general agreement has not been reached regarding the acute modulation of autonomic function. Aim: The present study aimed at revealing the acute effect of yoga on the autonomic activity using heart rate variability (HRV) measurement. Methods: Twenty-seven healthy controls participated in the present study. Fifteen of them (39.5 ± 8.5 years old) were naïve and 12 (45.1 ± 7.0 years old) were experienced in yoga. Yoga skills included breath awareness, two types of asana, and two types of pranayama. HRV was measured at the baseline, during yoga, and at the resting state after yoga. Results: In both yoga-naïve and experienced participants, the changes in low-frequency (LF) component of HRV and its ratio to high-frequency (HF) component (LF/HF) after yoga were found to be correlated negatively with the baseline data. The changes in LF after yoga were also correlated with LF during yoga. The changes in HF as well as the raw HRV data after yoga were not related to the baseline HRV or the HRV during yoga. Conclusion: The results indicate that yoga leads to an increase in LF when LF is low and leads to a decrease in LF when it is high at the baseline. This normalization of LF is dependent on the autonomic modulation during yoga and may underlie the clinical effectiveness of yoga therapy both in yoga-naïve and experienced subjects. [ABSTRACT FROM AUTHOR]