Physiological alterations in cortical neurons are induced during adaptation to an artificial scotoma, a small homogeneous patch within a dynamic random noise or patterned background. When the dynamic noise is replaced by an equiluminant gray background, a twinkling aftereffect can be seen in the location of the artificial scotoma. Following binocular adaptation, we discovered that the perceived size of the twinkling aftereffect was dramatically smaller than the inducing artificial scotoma. Dichoptic adaptation induced shrinkage in the twinkling aftereffect that was similar to that found after binocular adaptation, suggesting that the twinkling aftereffect and its shrinkage both have cortical origins. We speculate that this perceptual shrinkage may reflect the interaction between two cortical mechanisms: a twinkling aftereffect mechanism that spreads throughout the artificial scotoma, and a filling-in mechanism that has a greater influence at the edges of the artificial scotoma and spreads inwards.