New developments in brain imaging lead to a better understanding of cortical and subcortical processes involved in pain perception and the establishment of chronic pain. For different forms of chronic pain long-term changes in cortical structures have been described. In patients with phantom limb pain and back pain alterations in the somatotopic organization of the primary somatosensory (SI) could be observed. The amount of this reorganization is correlated with the subjective pain rating. These changes, which are based on processes of neuronal plasticity, can partially be reversed by analgesic interventions. For the investigation of cortical processes concerning reorganization, EEG and MEG methods are most suitable because of their high temporal and spatial resolution. In conclusion, these findings open a new way for therapeutic interventions to prevent the development of chronic pain.