Traditionally, the medial temporal lobe (MTL) was linked to explicit or declarative memory in associative learning. However, recent studies have reported MTL involvement even when volunteers are not consciously aware of the learned contingencies. Therefore, the mechanism of the MTL-related learning process cannot be described sufficiently by the explicit/implicit distinction, and the underlying process in the MTL for associative learning needs a more functional characterization. A possible feature that would allow a functional specification also for implicit learning is the nature of the material that is learned. Given that implicit memory tasks often comprise a combination of perceptual and motor learning, we hypothesized that implicit learning of the perceptual but not the motor component entails MTL activation in these studies. To directly test this hypothesis, we designed a purely perceptual and a purely motor variant of the serial reaction time task. In two groups of human volunteers, behavioral results clearly showed that both variants were learned without awareness. Neuronal recordings using fMRI revealed that bilateral hippocampal activation was observed only for implicit learning of the perceptual sequence, not for the motor sequence. This dissociation clearly shows that the functional role of the hippocampus for learning is determined by the domain of the learned association and that the function of the medial temporal lobe system is the processing of contingencies between perceptual features regardless of the explicit or implicit nature of the ensuing memory.