Effects of anodal transcranial direct current stimulation (tDCS) of the motor cortex on heart rate variability (HRV) indices in healthy volunteers were examined. Baseline HRVs of 16 healthy subjects were recorded, and the HRV changes during anodal and sham tDCS stimulation over the vertex were observed. RM-ANOVA showed significant changes in the means of the high-frequency (HF) band, lowfrequency (LF) band, and LF/HF ratio (P < 0.0001, P = 0.012, and P = 0.01, respectively). A significant decrease in the LF/HF ratio was found during tDCS as compared to baseline (P = 0.033); this effect was mainly due to an increase in the HF band during active stimulation (P = 0.002 in active vs. baseline, and P = 0.007 in active vs. sham). A slight statistically insignificant decrease in the LF band and increase in the HF band induced a significance in comparison of the LF/HF ratio during sham stimulation. The increase in the HF HRV component reflects intensification of parasympathetic activity during anodal stimulation of the motor cortex. Possible explanations are activation of the motor cortex or a dominancy of the left hemisphere due to lateralized current flow. According to our results, neuromodulation of the motor cortex can be an adjuvant to maintain the autonomic balance in some neurological diseases.