The primate visual system incorporates a highly specialized subsystem for the analysis of motion in the visual field. A key element of this subsystem is the middle temporal (MT) cortical area, which contains a majority of direction-selective neurons. MT neurons are also selective for binocular disparity (depth), which is perplexing given that they are not sensitive to motion through depth. What is the role of disparity in MT? Our data suggest an important link between disparity and transparent motion detection. Motion signals in different directions tend to inhibit each other within a given MT receptive field. This inhibition has an averaging effect which minimizes MT responses to random motion signals created by light intensity changes and other non-motion stimuli (motion noise). But, in the absence of disparity cues, inhibition may also occur between surfaces moving in different directions through the same part of the visual field (transparent motion), thus impairing the detection of either surface. Here we show that inhibition in MT occurs mainly between motion signals with similar disparities. Transparent surface movements at different depths are thus represented independently in MT (that is, without inhibiting each other) whereas spurious motion signals from a given surface tend to cancel out. To our knowledge, these results provide the first evidence for a functional integration of motion and disparity in MT.