Transcranial magnetic stimulation (TMS) has served as an important technological breakthrough in the field of the physiology of movement disorders over the last three decades. TMS has grown popular owing to the ease of application as well as its painless and noninvasive character. The technique has provide important insights into understanding the pathophysiology of movement disorders, particularly Parkinson's disease and dystonia. The basic applications have included the study of motor cortex excitability, functioning of excitatory and inhibitory circuits, study of interactions between sensory and motor systems, and the plasticity response of the brain. TMS has also made important contributions to understanding the response to treatments such as dopaminergic medications, botulinum toxin injections, and deep brain stimulation surgery. This review summarizes the knowledge gained to date with TMS in Parkinson's disease and dystonia, and highlights the current challenges in the use of TMS technology.