Depth perception is better when observers view stimuli containing a mixture of bright and dark visual features. It is currently unclear where in the visual system sensory processing benefits from the availability of different contrast polarity. To address this question, we applied transcranial magnetic stimulation to the visual cortex to modulate normal neural activity during processing of single- or mixed-polarity random-dot stereograms. In line with previous work, participants gave significantly better depth judgments for mixed-polarity stimuli. Stimulation of early visual cortex (V1/V2) significantly increased this benefit for mixed-polarity stimuli, and it did not affect performance for single-polarity stimuli. Stimulation of disparity responsive areas V3a and LO had no effect on perception. Our findings show that disparity processing in early visual cortex gives rise to the mixed-polarity benefit. This is consistent with computational models of stereopsis at the level of V1 that produce a mixed polarity benefit.