When a featureless achromatic target is placed on a textured pattern and steadily viewed in peripheral vision, after a few seconds it seems to fill-in with the surrounding texture, similar to the perceptual experience of patients with scotomas from damage to the visual pathways. Such "artificial scotomas" are thought to arise early in visual processing, but their neural basis in humans has not been fully explored. Here we used functional MRI to show that perceptual completion of an artificial scotoma is associated with selective reductions in activity in the retinotopic representation of the target in human primary visual cortex (V1) and area V2. Moreover, the persistence of signals associated with the target, even after perceptual completion had been reported, indicate the presence of a persistent representation of the now invisible target.