Under transparent motion conditions overlapping surfaces are perceived simultaneously, each with its own direction. The motion aftereffect (MAE) of transparent motion, however, is undirectional and its direction is opposite to that of a sensitivity-weighted vector sum of both inducing vectors. Here we report a bidirectional and transparent MAE contingent on binocular disparity. Depth (from retinal disparity) was introduced between two patterns. A fixation dot was presented at zero disparity, that is, located between the two adaptation patterns. After adaptation to such a stimulus configuration testing was carried out with two stationary test patterns at the same depths as the preceding moving patterns. For opposite directions a clear transparent MAE was perceived. However, if the adaptation directions were orthogonal the chance of a transparent MAE being perceived decreased substantially. This was subject dependent. Some subjects perceived an orthogonal transparent MAE whereas others saw the negative vector sum-an integrated MAE. In addition the behavior of the MAE when the distance in depth between adapting and test patterns was increased was investigated: it was found that the visibility of the MAE then decreased. Visibility is defined in this paper as: (i) the percentage of the trials in which MAEs are perceived and (ii) the average MAE duration. Both measures decreased with increasing distance. The results suggest that segregation and integration may be mediated by direction-tuned channels that interact with disparity-tuned channels.