This study was undertaken to determine the functional properties of neurons in the anatomically altered somatosensory cortex after neonatal whisker damage. In mice and rats neonatal lesions of the facial vibrissae change the anatomical organization of barrels in the contralateral SmI cortex. These changes depend on the pattern and severity of the peripheral damage and the developmental age of the animals. To understand some of the functional correlates of these anatomical changes, the middle row of vibrissae (row C) was damaged in mice on postnatal days 1, 3, and 5 and in rats on postnatal days 1 and 5. The receptive field properties of single cortical units were studied after the animals matured. In 24 mice and 15 rats a total of 1,370 units were characterized in microelectrode penetrations which passed through the somatosensory cortex either tangential or perpendicular to the pia. Units were localized anatomically with respect to both barrel and laminar boundaries, and the extent of the peripheral damage was assessed histologically. The data revealed an orderly representation of the sensory periphery that coincided with the altered cytoarchitectonic organization of the SmI cortex. Specifically: (1) Units in the enlarged row B or row D barrels responded primarily to row B or row D whiskers. (2) In layer IV, units in the altered row C cortex either could not be reliably driven from the periphery, were activated by stimulation of scar tissue in the damaged facial row C, or were driven by adjacent, intact row B or row D whiskers. (3) Units in supra- and infragranular layers either had no row C representation or incorporated scar tissue in their receptive fields in a topographically correct fashion. Responses of units to stimulation of scar tissue were qualitatively similar to those elicited from intact vibrissae, which also activated them. (4) In SmII, units that responded to whiskers had receptive fields whose organization matched the representation of the periphery observed in SmI. (5) There was no mapping of nonmystacial pad structures in the barrel cortex, and there were no units with abnormal multiwhisker interactions when laminar boundaries were taken into account. These data indicate that neonatal damage to the whiskers alters both the anatomical arrangement of the barrels and the physiologically determined somatotopic representation of the sensory periphery in a parallel and predictable fashion.