The borders between objects and their backgrounds create discontinuities in image feature maps that can be used to recover object shape. Here we used functional magnetic resonance imaging to identify cortical areas that encode two of the most important image segmentation cues: relative motion and relative disparity. Relative motion and disparity cues were isolated by defining a central 2-degree disk using random-dot kinematograms and stereograms, respectively. For motion, the disk elicited retinotopically organized activations starting in V1 and extending through V2 and V3. In the surrounding region, we observed phase-inverted activations indicative of suppression, extending out to at least 6 degrees of retinal eccentricity. For disparity, disk activations were only found in V3, while suppression was observed in all early visual areas. Outside of early visual cortex, several areas were sensitive to both types of cues, most notably LO1, LO2 and V3B, making them additional candidate areas for motion- and disparity-cue combination. Adding an orthogonal task at fixation did not diminish these effects, and in fact led to small but measurable disk activations in V1 and V2 for disparity. The overall pattern of extra-striate activations is consistent with recent three-stream models of cortical organization.