Filling-in refers to the tendency of stabilized retinal stimuli to fade and become replaced by their background. This phenomenon is a good example of central brain mechanisms that can selectively add or delete information to/from the retinal input. Importantly, such cortical mechanisms may overlap with those that are used more generally in visual perception. In order to identify cortical areas that contribute to perceptual filling-in, we used functional magnetic resonance imaging to image activity in the visual cortex while subjects experienced filling-in. Nine subjects viewed an achromatic disc with slightly higher luminance than the background and indicated the presence or absence of filling-in by a keypress. The disc was placed in either the upper or lower left quadrant. Similar high-contrast stimuli were used to map out the retinotopic representation of the disc. Unexpectedly, the lower-field high-contrast stimulus produced more parietal cortex activation than the upper-field condition, indicating preferential representation of the lower field by attentional control mechanisms. During perceptual filling-in, we observed significant contralateral reductions in activation in lower-tier retinotopic areas V1 and V2. In contrast, increased activation was consistently observed in visual areas V3A and V4v, higher-level cortex in the intraparietal sulcus, posterior superior temporal sulcus, and the ventral occipital–temporal region, as well as the pulvinar. The filling-in activation pattern was remarkably similar for both the upper- and lower-field conditions. Behaviorally, filling-in was reported to be easier for the lower visual field, and filling-in periods were longer for the lower than the upper quadrant. We suggest this behavioral asymmetry may be partially due to the preferential parietal representation of the lower field. The results lead us to propose that perceptual filling-in recruits high-level control mechanisms to reconcile competing percepts, and alters the normal image-related signals at the first stages of cortical processing. Moreover, the overall pattern of activation during filling-in resembles that seen in other studies of perceptually bistable stimuli, including binocular rivalry, indicating common control mechanisms.