Studies of human classification learning using functional neuroimaging have suggested that basal ganglia and medial temporal lobe memory systems may interact during learning. We review these results and outline a set of possible mechanisms for such interactions. Effective connectivity analyses suggest that interaction between basal ganglia and medial temporal lobe are mediated by prefrontal cortex rather than by direct connectivity between regions. A review of possible neurobiological mechanisms suggests that interactions may be driven by neuromodulatory systems in addition to mediation by interaction of inputs to prefrontal cortical neurons. These results suggest that memory system interactions may reflect multiple mechanisms that combine to optimize behavior based on experience.