Transcranial magnetic stimulation (TMS) can be used to investigate the intracortical circuits within the primary motor cortex (M1) and connections from other cortical areas to the M1. Repetitive TMS (rTMS) is able to modify the cortical excitability and can be used to test the cortical plasticity. In Parkinson’s disease (PD), there are impairments in intracortical circuits, indicating abnormal modulation of M1 excitability by intrahemispheric and interhemispheric inputs. Organic and psychogenic dystonia may have similar impairment in intracortical circuits but may have differences in cortical plasticity. Essential tremor and PD tremor respond differently to a resetting stimulus applied to different sites along the pathway for tremor generation and transmission, suggesting that they have different pathophysiological origins. Intracortical circuits may be impaired in Tourette’s syndrome but tend to normalize during task performance. Repeated applications of rTMS may induce long-term changes in cortical excitability. It is being developed as a potential treatment to normalize cortical excitability and intracortical circuits for movement disorders.