We investigated how the cortical representation of a stimulus is altered by conscious experience. To this end, we used object substitution masking to manipulate conscious awareness, in conjunction with an fMRI-adaptation paradigm to evaluate how the internal representation of the stimulus is altered. In each trial of the experiment, the adapting stimulus was a notched diamond with the top, bottom, left, or right corner removed. This stimulus was presented randomly to one of four spatial locations, introducing the spatial ambiguity considered necessary for object substitution masking. The adapting stimulus was then immediately masked by four dots surrounding the stimulus. Following the masked stimulus, a second notched diamond, either the same or different in orientation from the adapting stimulus, was presented to test for adaptation. The subjects’ task was to report the orientation of the notch for the adapting stimulus (i.e., the masked presentation), which was either consciously perceived by the observer or not, depending on whether masking was successful. Trials were binned post hoc according to the correctness of the response for analysis of the functional imaging data. In separate functional imaging runs, we independently identified the four regions corresponding to the four stimulus locations in primary visual cortex (V1), and lateral occipital cortex (LO). In V1, the cortical responses for correct and incorrect trials did not differ significantly. The response in LO, however, was dependent on the subjects’ conscious experience: Trials on which subjects correctly reported the orientation of the notch evidenced attenuation of the hemodynamic response for repeated presentations, whereas incorrect trials did not. These results indicate that the cortical representation of a stimulus in LO is shaped by an observer’s conscious experience, whereas the representation in V1 is not.