One has to face numerous difficulties when trying to establish a dissociation between conscious and unconscious knowledge. In this paper, we review several of these problems as well as the different methodological solutions that have been proposed to address them. We suggest that each of the different methodological solutions offered refers to a different operational definition of consciousness, and present empirical examples of sequence learning studies in which these different procedures were applied to differentiate between implicit and explicit knowledge acquisition. We also show how the use of a sensitive behavioral method, the process dissociation procedure, confers a distinctive advantage in brain-imaging studies when aiming to delineate the neural correlates of conscious and unconscious processes in sequence learning.