It has been suggested that the cortico-striatal system might play a crucial role in learning behavioural plans of action. We have tested this hypothesis by studying the dynamics of functional coupling among the neural elements of cortico-striatal circuitry. Human cerebral activity was measured with functional magnetic resonance imaging (fMRI) during the learning of an associative visuomotor task. Structural equation modelling of regional fMRI time-series was used to characterize learning-related changes in effective connectivity. We report that learning to associate visual instructions with motor responses significantly altered cortico-striatal functional couplings. Specific learning-related increases of effective connectivity were found in temporo-striatal and fronto-striatal circuits. Connectivity among portions of the frontal cortex decreased as a function of learning. Temporo-frontal and parieto-frontal couplings were not altered during learning. We infer that novel visuomotor associations are established through the enhancement of specific cortico-striatal circuits, rather than through the alteration of direct temporo-frontal or parieto-frontal connectivity.