Transcranial magnetic stimulation (TMS) and repetitive TMS (rTMS) are indirect and noninvasive methods used to induce excitability changes in the motor cortex via a wire coil generating magnetic field passes through the scalp in humans. Today, TMS has become a key method to investigate brain functioning in humans. Moreover as rTMS can lead to long-lasting aftereffects in the brain, it is thought to be able to induce plasticity. This appears to be a potential therapeutic tool for neurological and psychiatric diseases. However, the physiological mechanisms underlying the effects induced by TMS and rTMS have not yet been clearly identified. The purpose of the present review is to bring together the main knowledge available on TMS and rTMS allowing an understanding of their mode of action and to specify the different parameters that influence their effects. This review takes an inventory of rTMS paradigms the most used in clinical research and exhibits the hypotheses commonly assumed to explain rTMS aftereffects.