Numerous imaging studies have contributed to the localization of motion-sensitive areas in the human brain. It is, however, still unclear how these areas contribute to global motion perception. Here, we investigate with functional MRI whether the motion-sensitive area hMT+/V5 is involved in perceptual segmentation and integration of motion signals. Stimuli were overlapping moving gratings that can be perceived either as two independently moving, transparent surfaces or as a single surface moving in an intermediate direction. We examined whether motion-sensitive area hMT+/V5 is involved in mediating the switches between the two percepts. The data show differential activation of hMT+/V5 with perceptual switches, suggesting that these are associated with a reconfiguration of cell assemblies in this area.