The basal ganglia have been implicated in diverse motor and cognitive functions, but there is still no model that can explain the full range of their contributions to behavior. I will describe recent results that challenge traditional assumptions in the field and describe a new model of the basal ganglia based on the principles of hierarchical control. According to this model, the cerebral cortex and basal ganglia implement transition control, in particular the rate of change in various perceptual configurations. The basal ganglia outputs, in turn, adjust the reference signals of position controllers in the midbrain and brainstem. This model can explain a rich variety of experimental findings and clinical symptoms.