Transcranial Magnetic Stimulation has been used for over 20 years to investigate recovery of motor function in stroke patients. In particular, it has been used to quantify the extent of damage to the corticospinal output, reorganisation of the cortical representation of the affected body parts and excitability of intracortical and cortico-cortical circuitries in both hemispheres. In this review, we provide a detailed account of most of the published data with particular reference to methodological issues that affect their interpretation.