We used optical imaging of intrinsic signals to characterize the functional representations of mystacial vibrissae (whiskers) in rat somatosensory cortex. Stimulation of individual whiskers for 2 s at 5 Hz resulted in a discrete area of functional activity in the cortex. Images of whisker representations were collected both through the dura and through a thinned skull. We characterized the functional representation of a whisker both spatially and temporally with two-dimensional images and three-dimensional surface plots of intrinsic signal development in the cortex in response to whisker stimulation. Single unit recordings verified that the representation of the whisker obtained with optical imaging corresponded with the electrophysiological response area of that whisker in the cortex. Lesions in the center of the functional activity were found to be in the center of the dense cytochrome oxidase patch for the corresponding whisker. In addition, a 3 x 3 matrix of whiskers was stimulated and the distances between the centers of the imaged representations and the distances between the centers of the layer IV cytochrome oxidase staining of the nine whiskers were found to be highly correlated (r = 0.98). This study shows a striking correspondence among imaging, physiology, and anatomy in the rat somatosensory cortex. Furthermore, the ability to use optical imaging through a thinned skull should allow investigations into the long-term changes in a sensory representation within a single animal.