Tourette's syndrome is characterized by simple, involuntary muscle contractions and/or more complex movements or stereotyped behaviors, including vocalizations. There are strong indications that the basal ganglia play an important role in the pathophysiology of Tourette's syndrome. The present account reviews the functional anatomy of the basal ganglia, with an emphasis on the prefrontal cortex-ventral striatopallidal system. Different parts of the basal ganglia and thalamocortical system, with a focus on the premotor and prefrontal cortices, are connected with each other via parallel, functionally segregated basal ganglia-thalamocortical systems. These parallel circuits, representing sensorimotor, cognitive and emotional-motivational behavioral processes, are connected with each other through specific pathways that serve to integrate these various functions. In the context of the discussion on the pathophysiological mechanisms that lead to the expression of tics, emphasis is placed on the pathways that lead from the ventral striatum via the dopaminergic substantia nigra to the dorsal striatum. The dorsal striatum is crucial for habit formation. A conclusion of this overview of the anatomical organization of the basal ganglia is that via dopaminergic pathways limbic-relation information can influence the expression of (fragments of) motor and behavioral repertoires. Whether such mechanisms indeed play a role in the expression of tics in Tourette's syndrome remains to be established.