The development of the rat barrel field cortex was investigated with an antibody to the axonal membrane-specific phosphoprotein GAP-43 in order to examine the developmental pattern of afferent projections, and with cytochrome oxidase histochemistry and Nissl stains to reveal the morphogenesis of cortical barrels. On the first two days after birth, GAP-43 immunostaining in the cortical plate was light and diffuse, then became intense in the presumptive layer IV of the parietal cortex on PND3 (day of birth = PND0). Immunoreactive densities were visible as small, focal patches within the centers of prospective barrels. These densities increased in size and intensity over the next few days and then diminished abruptly. On PND7, the distribution of GAP-43 was coextensive with barrels, as defined by cytochrome oxidase histochemistry and Nissl staining. GAP-43 virtually disappeared from the barrels after PND7. From the second postnatal week, GAP-43 immunostaining was evident in the septa between barrels and in the dysgranular regions of SI cortex. This pattern of GAP-43 distribution was complementary to the pattern of cytochrome oxidase activity, and persisted into maturity. In an attempt to identify possible source(s) of GAP-43 positive afferents in the developing barrels, we examined the effects of altering the sensory periphery on the distribution of GAP-43 immunostaining in the cortex. Rat pups had row C whiskers cauterized on PND0 and were sacrificed on PND3 or PND5. Whereas immunopositive densities corresponding to intact whiskers developed in a normal, punctate pattern, cortical representation of the lesioned whiskers formed a continuous band of labeling that was evident as early as PND3. We argue that the disjunctive expression of GAP-43 in the barrel field reflects the pattern of distribution of afferents (most likely from the ventro-basal thalamic nucleus) to the barrel field cortex, and that this pattern may be instructive in the formation of barrels as cytoarchitectonic units. The rapid alteration in patterns of immunostaining following whisker lesions lends further support to the conclusion that the "barrel template" is conveyed to the neocortex by incoming afferents. The possible significance of the transient expression of GAP-43 in the maturing barrel field is discussed.