The large mystacial vibrissae on the faces of rodents have punctate representations in all stations in the central trigeminal pathway, including layer IV of the somatosensory cortex (SmI). The cortical whisker correlates, multicellular units termed barrels, are not present at birth, and damage to the vibrissae during the first postnatal week results in altered adult cytoarchitectonics. The anatomical effects of vibrissae damage in the cortex have been well documented; here, we investigated the functional organization of altered SmI barrels with a high-resolution 2-deoxyglucose (2-DG) technique (Durham et al., '81, J. Neurosci. 1:519). The middle row of vibrissae was cauterized in 1-, 2-, 3-, 4-, or 5-day-old mice, and the animals were allowed to survive to sexual maturity. Various combinations of vibrissae were clipped acutely 24 hours prior to injection of 2-4 mCi of (3H)2-DG. Mice actively explored an empty cage for 60 minutes, stimulating the remaining vibrissae. The mice then were perfused and their brains prepared for paraffin histology and emulsion autoradiography. In tangential sections through layer IV, patterns of neuropil and cell body labeling were analyzed with respect to barrel cytoarchitecture in normal and vibrissae-damaged mice. In both control and experimental animals, patterns of neuropil and cell somata label corresponded exactly to barrel boundaries, whether normal or altered by vibrissae damage. Only those barrels for which vibrissae were intact had high levels of label, with anterior barrels more heavily labeled. Many neurons in the septa between these barrels and the adjacent barrels were labeled also. We found slightly higher neuropil label in the cortical zone corresponding to the damaged zone on the face in animals lesioned at any time. These data indicate that physiological somatotopy in vibrissae-damaged animals matches the anatomical cytoarchitecture.