In a previous functional magnetic resonance imaging (fMRI) study we demonstrated an involvement of the medial temporal lobe (MTL) during an implicit learning task. We concluded that the MTL was engaged because of the complex contingencies that were implicitly learned. In addition, the basal ganglia demonstrated effects of a paralleled proceduralization of fixed stimulus-response associations. In the present study we directly tested the hypothesis that the MTL activation depends upon implementing the complex regularity in task material, whereas activation of basal ganglia does not. Therefore, we rearranged task material such that it did not contain any complex regularity. The statistical comparison of behavioral and fMRI data between the materials allowed for isolating effects that were directly related to the implicit learning process regarding the complex regularity. The results showed a reliable difference of fMRI signal limited to the MTL, indicating a specific functional role of the MTL in implicit learning of complex contingencies. Furthermore, no difference of BOLD (Blood-Oxygenation Level Dependent) signal in the basal ganglia and cerebellum were detected, supporting the assumption of a functional involvement of the structures in proceduralization of simple stimulus-response associations but not in implicitly learning complex relations. We therefore conclude that the nature of the learned associations is relevant for determining the neuronal focus of learning, rather than the accompanying awareness. (Contains 2 tables and 4 figures.)