Visual scenes are frequently composed of objects that move in different directions. To segment such scenes into distinct objects or image planes, local motion cues have to be evaluated and integrated according to criteria of global coherence. When several populations of coherently moving random dots penetrate each other, the visual system tends to assign them to different planes-perceived as transparent motion. This process of integration was studied by changing the angle of motion trajectories with which groups of dots penetrate each other or by varying the spatial constellation of dots moving in opponent directions. Psychophysical testing revealed that stimuli providing almost identical local motion cues could be perceived in three very different ways: (1) as a matrix of stationary flickering dots, (2) as a single surface of coherently moving dots, and (3) as two transparent dot matrices moving in different directions. Behaviorally controlled functional magnetic resonance imaging (fMRI) was used to identify brain regions that contribute to the integration of local motion cues into coherently moving surfaces. Activation of the human motion complex (hMT+/V5) and of areas in the fusiform gyrus (FG) as well as in the intraparietal sulcus (IPS-occ) was correlated with the perception of coherent motion and especially hMT+/V5 took a central role in differentiating transparent motion from single-surface coherent motion.