We examined whether repetitive transcranial magnetic stimulation (rTMS) at a low rate could influence autonomic function, specially heart rate variability (HRV) by power spectrum analysis. We studied 16 healthy male volunteers as a stimulation group and 16 others as a sham group. The stimulation group received magnetic stimulations from a circular coil over Cz at a frequency of 0.2 Hz and an intensity presenting 90% of the motor threshold. Experiments in both groups included four daily sessions; at each, a train of 70 stimuli was delivered over 350 s. HRV of low-frequency power (LF) in a standing position and high-frequency power (HF) in a supine position were measured before and after each session. After stimulation, HF and LF powers were significantly increased. After sham stimulation, the power of HF but not that of LF significantly increased. Neither actual nor sham stimulation produced a long-term effect detectable on day 5. The finding of transiently increased LF power following actual but not sham stimulation suggests that rTMS may activate the sympathetic nervous system.