Although the general principles of axon guidance in vitro are understood, little is known about how axons respond to the myriad of cues in vivo and navigate axon pathways within the complex milieu of the embryonic brain. Although neuropilin-1 is an axon guidance receptor for chemorepulsive ligands in the class 3 subfamily of semaphorins, its role in directing axon growth in vivo is unknown. In the present study, we have examined the expression and role of neuropilin-1 in the embryonic forebrain of Xenopus. Neuropilin-1 was selectively expressed by a subset of axons in the early scaffold of axon tracts. These axons arise from the presumptive telencephalic nucleus, cross the rostral midline by means of the postoptic commissure, and enter the major longitudinal tract of the prosencephalon, the tract of the postoptic commissure. At the level of the mesencephalon, these axons diverge and enter one of two axon tracts: either the ventral longitudinal tract or the ventral commissure. This same population of axons also expresses NOC-2, a novel glycoform of the neural cell adhesion molecule N-CAM. We have previously revealed the presence of a chemorepulsive activity underlying the pathway followed by these axons as they cross the ventral commissure. When neuropilin-1 was overexpressed after blastomere injections of synthetic RNA transcripts, NOC-2 axons entered the ventral commissure but failed to cross the midline. Instead, these axons were inhibited from growing ventrally within the commissural pathway. These results suggest that the level of neuropilin-1 in the NOC-2 subpopulation of axons is critical for determining whether these axons reach the ventral midline. Thus, neuropilin-1 may a specific role in directing the growth of NOC-2 axons across the ventral midline in the early embryonic mesencephalon.