Tremendous advances in neuroimaging methods and analytic techniques hold great promise in providing the rehabilitation clinician with a much greater understanding of brain pathology and its potential influence on rehabilitation outcome. This special issues of NeuroRehabilitation overviews the field. Contemporary neuroimaging methods are reviewed specifically in traumatic brain injury (TBI), anoxic brain injury (ABI) and stroke. Innovative methods combined with standard quantitative metrics and traditional clinical assessment provide the rehabilitation clinician with multiple methods to best understand the nature and extent on underlying neuropathology and how to use this information in guiding rehabilitation therapies and predicting outcome.