Several human and monkey studies have demonstrated a close relationship between motion perception and activation of area V5, leading to the general view that activity in this area correlates with the subjective experience of motion. In the present study, we investigate whether the responses of this area are still governed by the motion percept when the latter is in conflict with the reality of the physical visual stimulation. We simultaneously presented two different, specially designed random-dot kinematograms, one to each eye. These stimuli either both had a single direction of motion and worked in synergy, or had opposite motion directions and thus cancelled each other out perceptually. In this way, we were able to pit the visual stimulus (one vs. two stimulating directions) against the reported perception (directional motion vs. motion noise) of human volunteers during fMRI experiments. We found that a strong motion stimulus that is weakly perceived is more effective in activating V5 (as well as V3) than a weaker motion stimulus, which is nevertheless robustly perceived. Thus, contrary to the prevailing view of perception being the correlate of activity in higher visual areas, we show here that activity is instead dominated by the properties of the physical stimulus, raising the question of whether there is a subpopulation of cells in V5 whose activity is critical for generating the motion percept. In addition, our results provide the first robust evidence for the presence of directionally selective neuronal populations in human prestriate cortex.