Whisker deflection conditioned stimuli (CS) were demonstrated to activate physiologically and anatomically defined barrels in the contralateral somatosensory cortex and to support trace-eyeblink conditioned responses when paired with corneal airpuff unconditioned stimuli in rabbits. Analysis of cytochrome-oxidase-stained somatosensory whisker-associated cortical barrels revealed a row-specific expansion of the conditioned compared with the nontrained hemisphere. This expansion was not evident in pseudo-conditioned rabbits, suggesting that this expansion of conditioned cortical barrels in response to a hippocampal- and forebrain-dependent learning task (trace conditioning) is associative rather than activity dependent. Using whisker stimulation as a CS in the well studied eyeblink conditioning paradigm will facilitate characterizing sensory cortical involvement in controlling and modulating an associatively learned response at the neural systems and cellular level.