We describe a procedure aimed to analyse Motor Evoked Potentials (MEPs) interhemispheric differences in motor excitability in a monohemispheric subacute stroke population. This protocol has specifically been oriented to scan for any differences in MEPs amplitude at rest and during contractions from a hand muscle, Abductor Digiti Minimi (ADM), after focal Transcranial Magnetic Stimulation (TMS) in both Affected (AH) and Unaffected (UH) Hemispheres. Stroke patients can be included in the protocol if they have suffered acute stroke during the two to four month period to the admission in our rehabilitation hospital. The purpose of this protocol is to establish whether any clear pattern of interhemispheric responsiveness exists and/or to define any possible correlation between MEPs and clinical data. Disability and neurological scores are evaluated to allow a numerical comparison with electrophysiological data. Two recording sessions are planned: the first when the selected patient is admitted (T1) and the second after 8 weeks (T2). Such a period has been arbitrarily chosen because it represents a reliable time after the first recording in order to observe clinical amelioration if present. Criteria for reproducibility of experimental conditions are illustrated.