In vertebrate embryos, neural crest cells migrate only through the anterior half of each somite while avoiding the posterior half. We demonstrate that neural crest cells express the receptor neuropilin 2 (Npn2), while its repulsive ligand semaphorin 3F (Sema3f) is restricted to the posterior-half somite. In Npn2 and Sema3f mutant mice, neural crest cells lose their segmental migration pattern and instead migrate as a uniform sheet, although somite polarity itself remains unchanged. Furthermore, Npn2 is cell autonomously required for neural crest cells to avoid Sema3f in vitro. These data show that Npn2/Sema3f signaling guides neural crest migration through the somite. Interestingly, neural crest cells still condense into segmentally arranged dorsal root ganglia in Npn2 nulls, suggesting that segmental neural crest migration and segmentation of the peripheral nervous system are separable processes.