The expression of the extracellular matrix molecules cytotactin, which is synthesized by glia, and cytotactin-binding (CTB) proteoglycan, which is synthesized by neurons, was examined in the developing brain of the mouse, specifically in the cortical barrel field, using highly specific polyclonal antibodies to the purified molecules. Both molecules appeared early in the development of the cortex but were excluded from the centers of the developing barrels at the time of entry and arborization of thalamocortical axons. Of the two major forms of cytotactin (220 and 200 kDa), the larger form predominated during development of the mouse brain and also predominated in mixed neuron-glia cultures but not in pure glial cultures. Both cytotactin and CTB proteoglycan were recognized by various lectins that have been shown in other studies to demarcate the barrel field: both molecules were recognized by lentil lectin and concanavalin A and CTB proteoglycan was also recognized by peanut and wheat germ agglutinins. The HNK-1 carbohydrate antigen, present on cytotactin, CTB proteoglycan, and other adhesion molecules, was also found in the barrel walls and diminished in the barrel hollows. Cytotactin and CTB proteoglycan were preferentially expressed in barrel walls through P12. After this time, their expression became uniform even though the histological pattern of barrel walls and hollows was maintained. The fusion of a row of barrels which results from peripheral damage to a row of whiskers was accompanied by the loss of patterned expression of both molecules following electrocauterization of a row of whisker follicles at P1.5. We conclude that activity from the periphery is important not only to development of anatomical pattern but also of the molecular pattern and that the expression of both glial and neuronal proteins can respond to such activity. The results are consistent with previous studies showing that incoming thalamocortical axons play a primary role in barrel field formation. They also suggest that both the migration of cortical neurons on glia and the refinement of the mapping between the peripheral whisker field and its cortical representation may depend upon the distribution of substrate adhesion molecules.