Preliminary studies suggest that stimulation of the motor cortex enhances motor recovery after stroke. Most of these studies employed transcranial magnetic stimulation of the brain and two different approaches have been evaluated. The first approach is based on the use of protocols of stimulation that increase cortical excitability, targeting the hemisphere in which the stroke occurred in order to enhance the output of the motor cortex and the response to physiotherapy. The second approach is based on the use of protocols of stimulation that suppress cortical excitability, targeting the intact hemisphere in order to counteract the imbalance due to the increased interhemispheric inhibition onto the lesioned cortex, and reducing the potential negative interference of the intact hemisphere with the function of the affected one. Cumulatively, preliminary studies suggest that transcranial magnetic stimulation might be a suitable method to combine with physiotherapy and improve recovery of useful limb function in stroke patients. However, further studies are needed to determine the best stimulation parameters and how to select patients who are likely to respond to this treatment.