Sensory information is encoded throughout the central nervous system by activation of specific groups of neurons. Neurons encoding information from a particular modality are grouped together and constitute an ordered neural representation or ''map'' of the stimulus. The organization of these representations is not static, but is capable of significant alteration in response to changes in the patterns of inputs delivered to the cortex in the appropriate behavioral context. Therefore, understanding the basic mechanisms that account for discontinuities in cortical representations are important for understanding both information processing in the cortex and plasticity of cortical organization. It is clear that both anatomic and physiologic mechanisms underlie both the genesis and the plasticity of these representations; however, their exact contributions are not fully understood. To examine neuronal anatomy around a representational border in rat primary somatosensory cortex (S1), a novel in vivo/in vitro preparation was used in which the location of the border between the forepaw and lower jaw representations in rat S1 was determined electrophysiologically and marked by dye iontophoresis in vivo. By using in vitro slices from the region in which this border was marked, the morphologies of single cortical layer 2/3 neurons close to and far from the border were determined by intracellular injection of biocytin. Neurons close to the border had dendritic arbors that were significantly biased away from the border; neurons far from the border did not. This bias was due to a decrease in the number of neurites that specifically crossed the border with a concomitant increase in other near-border parts of the neuron, consistent with the ideas that patterns of activity are important for neurite outgrowth and that neurons maintain a relatively constant total neurite extent. These findings confirm the close association of cortical anatomy and physiology and illustrate their relationships with cortical representational discontinuities.