Neurophysiological and neuroimaging studies suggest that pain may play a major role in determining cortical somatosensory rearrangements even in the adult brain. The re-organizational power of pain, however, has been tested in models in which massive deafferentation co-existed with pain (e.g. in phantom pain). Moreover, information on whether spinal and brainstem changes contribute to pain-related plasticity in humans is meagre. We used the non-invasive somatosensory evoked potentials technique in patients with right primary trigeminal neuralgia and no clinical signs of large-diameter fibers of trigeminal deafferentation to assess whether pain may induce plastic changes at multiple levels in the somatosensory system. Subcortical and cortical potentials evoked by stimulation of the right median and posterior tibial nerves ipsilateral to the facial pain were compared with those obtained following stimulation of the left median and tibial nerves and with those obtained in a control group tested in comparable conditions. Amplitudes of parietal N20 and P27 and frontal N30 potentials observed following stimulation of the right median nerve ipsilateral to the facial pain were greater than those of the left median nerve and showed a positive correlation with magnitude of pain. This right-left asymmetry was absent following stimulation of the patients' tibial nerves and in control subjects. No changes were found in spinal N13 and brainstem P14. That facial pain is associated with neuroplastic changes within the somatic cortical representation of the hand suggests a pain-related topographic cortical reorganisation.