Six months after stroke onset, 50 % of patients are still disabled and dependent, while many brain mechanisms of recovery remain partially unknown or misunderstood. However, brain imaging and cerebral connectivity analytical techniques have provided invaluable insights into such mechanisms and identified two main patterns of brain reorganization depending on stroke severity. The contralesional primary motor cortex can take over motor function in severely impaired patients, whereas the ipsilesional motor cortex or hemisphere reorganize themselves in good recoverers. These patterns evolve with time after stroke, and highlight ipsilesional and contralesional primary and secondary areas that appear to take over lost functions. The crucial role of these areas has been confirmed by histological tracer studies. In addition, non-invasive techniques can stimulate post-stroke brain plasticity, although appropriate targets first need to be found. Imaging has proved useful for finding such appropriate targets and has also provided biomarkers of efficacy with various therapies. Moreover, it has provided some clues to the mechanisms of action of recovery-enhancing drugs. These imaging techniques have also identified patients who show atypical reorganization and recovery patterns. Thus, it may be necessary to design individualized and targeted therapies.