Somatotopy is a fundamental concept that is essential for the understanding of the functions of the brain. Here, I have described somatotopy in the basal ganglia that comprise the striatum, subthalamic nucleus, globus pallidus, and substantia nigra. Projections from the motor cortical subregions that represent different body parts terminate in different regions of these nuclei. Basal ganglia neurons respond not only to the stimulation of the corresponding subregions of the motor cortices but also to the active and passive movements of the corresponding body parts. On the basis of these anatomical and physiological findings, somatotopy can be identified in the motor territories of these nuclei in the basal ganglia. In addition, projections from functionally interrelated cortical areas partially converge through a cortico-basal ganglia loop. Disorganized somatotopy may explain, at least in part, the pathophysiology of movement disorders such as Parkinson disease and dystonia.