Understanding the functional organization of the basal ganglia requires a broad array of complementary theoretical models. Although the basal ganglia operate as part of a system of parallel cortico-basal ganglia-thalamocortical loops, there is clearly integration between the loops and there are probably more of these loops than previously conceived. Moreover, modulation by external inputs, particularly from the brainstem (eg, pedunculopontine nucleus, raphe nucleus, and locus coeruleus) adds to the complexity of the system. We now appreciate that the organization of the basal ganglia is not static and shows significant plasticity that allows the ganglia to function in learning processes and in response to age or disease, either as components of the pathophysiology or as compensatory mechanisms to reduce the functional impact of disease.