The thalamocortical slice is widely employed for in vitro studies of cortical circuits. This preparation was developed in order to preserve anatomical and functional connectivity between the ventrobasal thalamus and somatosensory (whisker/barrel) cortex of young mice, and thalamocortical slice experiments have contributed significantly to our understanding of the thalamocortical synapse. Cortical somatotopy within thalamocortical slices, however, has not been characterized, and this greatly limits their use in studies that require identification of cortical areas associated with particular regions of the sensory periphery. To address this shortcoming we used electrophysiological recording and neuroanatomical labeling techniques in rats to mark the position of functionally defined whisker barrels, in vivo. We subsequently processed the brains in a plane appropriate for TC slices and characterized the location of somatotopically identified barrels in relation to other aspects of slice topology. We found that barrels associated with the large mobile whiskers occupy a particular location in TC slices, but that there are certain constraints to studying this portion of the barrelfield in vitro.