The functional role of different subcortical areas in sequence learning is not clear. In the current study, Parkinson's patients, patients with cerebellar damage, and age-matched control participants performed a serial reaction time task in which a spatial sequence and a temporal sequence were presented simultaneously. The responses were based on the spatial sequence, and the temporal sequence was incidental to the task. The two sequences were of the same length, and the phase relationship between them was held constant throughout training. Sequence learning was assessed comparing performance when both sequences were present versus when the dimension of interest was randomized. In addition, sequence integration was assessed by introducing phase-shift blocks. A functional dissociation was found between the two patient groups. Whereas the Parkinson's patients learned the spatial and temporal sequences individually, they did not learn the relationship between the two sequences, suggesting the basal ganglia play a functional role in sequence integration. In contrast, the cerebellar patients did not show any evidence of sequence learning at all, suggesting the cerebellum might play a general role in forming sequential associations.