This article reviews several protocols of repetitive transcranial magnetic stimulation (rTMS)-induced plasticity. rTMS, when applied to the motor cortex or other cortical regions of the brain, may induce effects that outlast the stimulation period. The neural plasticity, which emerges as a result of such interventions, has been studied to gain insight into plasticity mechanisms of the brain. In two protocols the structure of rTMS trains is modified, informed by the knowledge of the physiological properties of the corticospinal system. Pulse configuration, stimulus frequency, stimulus intensity, the duration of the application period, and the total number of stimuli are some variables that have to be taken into account when reviewing the physiological effects of rTMS. This article also introduces the concept of patterned rTMS pulses and rTMS with ischemic nerve block. In addition, rTMS has raised considerable interest because of its therapeutic potential; however, much needs to be done in this field.