Interactions between growing axons are considered to play important roles for the establishment of precise neuronal connections during the development of the nervous system. Here we used time-lapse imaging techniques to examine the behavior of neocortical and thalamic axons when they encounter each other in vitro. Results indicate that axonal growth cones are able to respond to specific cues expressed on the surface of fibers. Thalamic growth cones often extended along the surface of other thalamic axons and, likewise, cortical growth cones formed fascicles with cortical axons. In contrast, after contacts between cortical and thalamic fibers, in most cases growth cones collapsed and retracted from the axons. Collapse assays using membrane preparations from cortical or thalamic explants demonstrated the existence of cell-type specific collapsing factors whose activity was enhanced by a member of the semaphorin protein family, Sema3A (expressed in the thalamocortical pathway), as it increased the rate of homotypic fasciculations and at the same time amplified the segregation between cortical and thalamic axons. The interaction between axonal surface molecules and environmental cues might mediate the segregation of afferent and efferent fiber tracts in the neocortical white matter.