Human somatosensory cortex (S1) is capable of rapid modification after temporary peripheral deafferentation but it is not known whether subcortical changes contribute to this modulation. We recorded spinal, brainstem and cortical somatosensory evoked potentials (SEPs) to median nerve stimulation following anaesthetic block of the ipsilateral ulnar nerve. Spinal N13 and subcortical P14, N18 potentials remained unchanged during the experiment. N20/P20, P27 and N30 cortical potentials, which are generated in different subareas of the S1 (N20/P20, N30 in area 3b; P27 in area 1), showed different increases in amplitude during the anaesthesia, which were more marked for N20/P20 and N30 than for P27 potentials. These results suggest that changes in S1 neural activity induced by transient deafferentation may be primarily intracortical in origin and appear to be segregated within the different subareas of the somatosensory cortex. Unmasking of pre-existing thalamo-cortical projections from median nerve territories, induced by ipsilateral ulnar nerve deafferentation, may be the mechanism underlying cortical SEP enhancement.