Early stages of the visual system respond to very rapid changes in visual input. By the time signals reach perception, this high temporal resolution is lost. We presented a rapidly counterphasing, masked grating that was invisible to observers. When asked to discern the orientation of the grating in a 2 alternative forced-choice procedure, observers performed at chance levels. These invisible gratings nevertheless caused a specific reduction in sensitivity to subsequently presented test gratings that were oriented parallel to the invisible grating. This adaptation effect allowed observers in a separate experiment to ascertain the orientation of the invisible grating on the basis of its effects on the appearance of the subsequent test gratings. Further to this, when a rapidly modulating adapting grating is presented to one eye, and adaptation is tested in the other eye, the level of adaptation is only about 20% smaller than if both stimuli were presented to both eyes. Taken together, the results imply that 1) the site of adaptation is no earlier than input layers of V1 (where orientation is first encoded) with a significant portion of adaptation being mediated at or beyond the stage where input from both eyes is integrated, 2) sensitivity to rapid change penetrates to this level, and 3) the neural mechanisms driving conscious perception either ignore, or do not have access to the information about rapid modulations that drive the adaptation effect.