Repetitive transcranial magnetic stimulation (rTMS) has been proposed as a possible treatment for psychiatric and neurological disorders characterized by focal brain excitability, such as major depression and action myoclonus. However, the mechanism of modulating excitability by rTMS is unclear. We examined the changes in high frequency oscillations (HFOs) of somatosensory evoked potentials (SEPs) before and after slow rTMS over the right primary somatosensory cortex (0.5 Hz, 50 pulses, 80% motor threshold intensity). The HFOs, which represent a localized activity of intracortical inhibitory interneurons, were significantly increased after slow rTMS, while the SEPs were not changed. Our results suggest that slow rTMS affects cortical excitability by modulating the activity of the intracortical inhibitory interneurons beyond the time of the stimulation and that rTMS may have therapeutic effects on such disorders.