The neural substrate of sequence learning is well known. However, we lack a clear understanding of the detailed functional properties of many of the areas involved. The reason for this discrepancy lies, in part, in the fact that two types of processes, implicit and explicit, subserve motor sequence learning, and these often interact with each other. The most significant recent advances have been the elucidation of the very complex relationships between medial motor areas and the temporal and ordinal control of sequences, and the demonstration that motor cortex is an important site for sequence storage and production. The challenge for the future will be to develop a coherent and internally consistent theory of sequence control.