Background: The basal ganglia-thalamo-cortical circuits are viewed as segregated parallel feed back loops, crucially involved in motor control. We have previously studied the subcortical activation pattern preceeding an automated four digit finger sequence, that was either self-initiated or triggered externally by a visual cue (Boecker et al., Neuroimage 2007). The anterior putamen, contralateral to the effector hand, was differentially more activated during the self-initiated condition, implicating its specific role in motor planning. In the present study, we extend these investigations on cognitive aspects of motor-processing. Specifically, we tested for the involvement of the anterior basal ganglia as part of the associative loop in a cognitive task, where novel movement sequences had to be generated, as opposed to the recall of an overlearned sequence.