When a visual scene allows multiple interpretations, the percepts may spontaneously alternate despite the stable retinal image and the invariant sensory input transmitted to the brain. To study the brain basis of such multi-stable percepts, we superimposed rapidly changing dynamic noise as regional tags to the Rubin vase-face figure and followed the corresponding tag-related cortical signals with magnetoencephalography. The activity already in the earliest visual cortical areas, the primary visual cortex included, varied with the perceptual states reported by the observers. These percept-related modulations most likely reflect top-down influences that accentuate the neural representation of the perceived object in the early visual cortex and maintain the segregation of objects from the background.