Motor dysfunction and recovery following stroke and rehabilitation are associated with primary motor cortex plasticity. To better track these effects we studied two patients with sub-acute sub-cortical stroke causing hemiparesis, who underwent an effective behavioral treatment termed Constraint Induced Movement Therapy (CIMT). The therapy involves 2 weeks of intensive motor training of the hemiparetic limb coupled with immobilization of the unaffected limb. The study included a longitudinal series of clinical evaluations and fMRI scans, before and after the treatment. The fMRI task included wrist, elbow, or ankle movements. Activity in the M1 upper-limb region of control subjects was stable, strictly contralateral, and similar in amplitude for elbow and wrist movements. These findings reflect the well-known contralateral motor control and support the idea of overlapping representations of adjacent joints in M1. In both patients, pre-CIMT activation patterns in M1 were tested twice and did not change significantly, were contralateral, and included elbow-wrist differences. Following CIMT, the clinical condition of both patients improved and three fMRI-explored prototypes were found: First, cluster position remained constant; Second, ipsilateral activity appeared in the unaffected hemispheres during hemiparetic movements; Third, patient-specific elbow-wrist inter and intra hemispheric differences were modified. All effects were long-lasting. We suggest that overlapping representations of adjacent joints contributed to the cortical plasticity observed following CIMT. Our findings should be confirmed by studying larger groups of homogeneous patients. Nevertheless, this study introduces multi-joint imaging studies and shows that it is both possible and valuable to carry it out in stroke patients.