Rehabilitation represents one of the key options available in the treatment of patients with motor deficits, whether they are acquired due to disease/brain injury or congenital in nature. Rehabilitation exploits the natural capacity of the brain to reorganize its structure, function, and connectivity. Despite its clear relevance in patient treatment, motor rehabilitation is often carried out in an ad hoc manner and its exact effects on the brain remain relatively poorly understood. In this regard, functional magnetic resonance imaging (fMRI) can be highly informative in the pre-intervention phase to evaluate the impact of a lesion or of a disease on the functioning of the motor network. This type of evaluation can be important for the subsequent tailoring of the rehabilitation intervention. Moreover, in a post-rehabilitation context, fMRI can be utilized to assess the possible mechanisms involved in the motor network reorganization following treatment. This in turn has strong implications for defining rehabilitation protocols for long-term monitoring of the mechanisms involved in treatment efficacy and possibly in the detection of pre-treatment functional features of the motor network able to predict the rehabilitative outcome