The striatum, which is the major component of the basal ganglia, displays a complex mosaic organization of neurochemical systems that are related to its neuroanatomical connections. This mosaic organization reflects multiple levels of functional compartments. The first level is determined by the segregation of two major striatal output systems, one to the globus pallidus (external segment) and the other to the entopeduncular nucleus and substantia nigra. The second level segregates the cortical outputs of sublaminae of layer V between the patch and matrix compartments of the striatum, which project to the dopaminergic and GABAergic neurons in the substantia nigra, respectively. The third level is related to the topography of cortical inputs by which regions of the striatum may be functionally defined on the basis of the cortical areas with which they are connected. Neurochemical markers display complex mosaic patterns in the striatum that, when examined in the context of the multi-level compartmental organization of the striatum, reveal the highly organized manner by which the striatum processes cortical information.