The development of the vertebrate neural crest presents a particularly challenging problem in pattern formation. Several studies have revealed that a population of neural crest cells penetrates the sclerotomal mesenchyme of the somite only in its rostral half. In a search for molecular correlates of this pattern, we have observed that cytotactin and a chondroitin sulfate proteoglycan, two interactive extracellular matrix molecules, show a specialized distribution within the sclerotome. Cytotactin was localized in the rostral half of the sclerotome at about the time of neural crest cell invasion. The proteoglycan was initially diffuse throughout the sclerotome but became restricted to the caudal half after the appearance of cytotactin and invasion of neural crest cells in the rostral half. These distributions were crest cell-independent; they occurred on the same schedule even when all crest cells were removed by surgical extirpation of the neural tube. Furthermore, in tissue culture, somite cells synthesized high levels of both molecules. In vitro, crest cells rounded up in the presence of these molecules and cell migration assays revealed that neither cytotactin nor proteoglycan alone was as good a substratum for crest cell migration as fibronectin. In combination with fibronectin, however, cytotactin or proteoglycan only restricted cell movement but did not prevent it. Taken together, these observations support the hypothesis that cytotactin and the chondroitin sulfate proteoglycan may contribute to pattern formation during embryogenesis by means of their site-restricted distribution, their ability to alter migration on other substrates such as fibronectin, and their ability to induce cell-surface modulation.