Neuroimaging plays an important role in acute stroke diagnosis and management, but it is not routinely used in rehabilitation settings. Incorporating imaging information in rehabilitation planning may eventually translate to better outcomes after stroke. Here we review the prediction of outcomes after stroke using magnetic resonance imaging. There are clear and specific relationships between the anatomy of the stroke lesion and impairments at the time of scanning, and at later time points in recovery. However, most studies demonstrate these relationships in groups of patients at the chronic stage. In order to be useful for rehabilitation, neuroimaging needs to provide prognostic information for individual patients at a much earlier stage. Recent studies have used diffusion tensor imaging and functional neuroimaging to address this, with promising results. Combining neuroimaging with clinical and neurophysiological assessments may also be useful. Future work in this area may support the tailoring of rehabilitation for individual patients based on their capacity for neural reorganization and recovery.