Transcranial magnetic stimulation (TMS) is a 20-year-old technique originally introduced to noninvasively investigate nervous propagation along the corticospinal tract, spinal roots, and peripheral nerves in humans. TMS is extensively used in clinical neurophysiology, including rehabilitation and intraoperative monitoring. Single-pulse TMS and other more recent versions (paired-pulse TMS, repetitive TMS, integration with structural and functional MRI, and neuronavigation) allow motor output to be mapped precisely to a given body district. Moreover, TMS can be used to evaluate excitatory/inhibitory intracortical circuits and to provide information on brain physiology and pathophysiology of various neuropsychiatric diseases as well as on the mechanisms of brain plasticity and of neuroactive drugs. TMS applied over nonmotor areas made it possible to extend research applications (often complementary with other functional neuroimaging techniques) in several fields of psychophysiology, causally testing brain–behavior relationships. Being able to induce relatively long-lasting excitability changes, repetitive TMS has made the treatment of neuropsychiatric diseases linked with brain excitability dysfunctions possible. These uses, however, warrant further large-scale studies. In emerging fields of research, TMS-EEG co-registration is considered a promising approach to evaluate corticocortical connectivity and brain reactivity with high temporal resolution. However, safety and ethical limitations of TMS technique need a high level of vigilance.