The present study aims to provide neurophysiological evidence of ipsilateral activation during motor recovery in patients after stroke. The effects of cortical reorganization were investigated using magnetic brain stimulation in order to record motor evoked potentials (MEPs) both from contralateral and ipsilateral hands. Ten healthy subjects and 13 patients were examined. The patients had suffered their first hemispheric stroke and consequent motor deficit. While ipsilateral responses (iMEPs) were absent in normal subjects, they were obtained from both ipsilateral and contralateral hands in patients. The ipsilateral MEP differed from contralateral MEP in the following respects: (1) elicitation during contraction; (2) a shorter latency; (3) a lower amplitude. The presence of optimal iMEPs (lower excitability threshold, larger amplitude) in recovered hands points to a role for the undamaged hemisphere, and in particular to the involvement of secondary motor areas. We suggest that iMEPs in general may be a marker of brain plasticity, and that the specific type described here appear in the context of fast autochthonous motor recovery.