Transcranial magnetic stimulation (TMS) provides a non-invasive method of induction of focal currents in the brain as well as transient modulation of the function of the targeted cortex. TMS is now widely used as a diagnostic tool in adults. In children, its application to date has been limited, even though TMS offers unique opportunities to gain insights into the neurophysiology of a child's brain. Using the single-pulse TMS technique, investigators can measure motor thresholds, motor evoked potentials, silent periods, central conduction times, and the paired-pulse curve to study central nervous system development and central motor reorganization after a cerebral lesion. Repetitive TMS (rTMS) is a novel treatment for psychiatric illness that is undergoing trials for a range of disorders in adults. Although there are rare published data on rTMS as a treatment for neuropsychiatric diseases in young persons, the benefits from TMS are nevertheless encouraging. Two important issues of pediatric TMS are safety considerations and methodology. In the future, rTMS may play an important role in the study and possibly in the therapy of children's diseases after more safety studies are completed.