Several authors within psychology, neuroscience and philosophy take for granted that standard empirical research techniques are applicable when studying consciousness. In this article, it is discussed whether one of the key methods in cognitive neuroscience – the contrastive analysis – suffers from any serious confounding when applied to the field of consciousness studies; that is to say, if there are any systematic difficulties when studying consciousness with this method that make the results untrustworthy. Through an analysis of theoretical arguments in favour of using contrastive analysis, combined with analyses of empirical findings, I conclude by arguing for three factors that currently are confounding of research using contrastive analysis. These are (1) unconscious processes, (2) introspective reports, and (3) attention.