Stereoscopic vision relies mainly on relative depth differences between objects rather than on their absolute distance in depth from where the eyes fixate. However, relative disparities are computed from absolute disparities, and it is not known where these two stages are represented in the human brain. Using functional MRI (fMRI), we assessed absolute and relative disparity selectivity with stereoscopic stimuli consisting of pairs of transparent planes in depth in which the absolute and relative disparity signals could be independently manipulated (at a local spatial scale). In experiment 1, relative disparity was kept constant, while absolute disparity was varied in one-half the blocks of trials ("mixed" blocks) and kept constant in the remaining one-half ("same" blocks), alternating between blocks. Because neuronal responses undergo adaptation and reduce their firing rate following repeated presentation of an effective stimulus, the fMRI signal reflecting activity of units selective for absolute disparity is expected to be smaller during "same" blocks as compared with "mixed" ones. Experiment 2 similarly manipulated relative disparity rather than absolute disparity. The results from both experiments were consistent with adaptation with differential effects across visual areas such that 1) dorsal areas (V3A, MT+/V5, V7) showed more adaptation to absolute than to relative disparity; 2) ventral areas (hV4, V8/V4alpha) showed an equal adaptation to both; and 3) early visual areas (V1, V2, V3) showed a small effect in both experiments. These results indicate that processing in dorsal areas may rely mostly on information about absolute disparities, while ventral areas split neural resources between the two types of stereoscopic information so as to maintain an important representation of relative disparity.