The aim of this study was to systematically review published data on the value of motor-evoked potentials (MEPs) in predicting motor recovery of the upper extremity and general functional outcome early after stroke. We searched PubMed for original prognostic studies. Only full-text original papers evaluating the prognostic value of MEPs elicited by transcranial magnetic stimulation (TMS) in motor function recovery of the upper extremity were included in this review. Data from the studies included in the review are presented in two tables: one shows the general characteristics of the studies and the other gives methodological details and results. Of 842 publications, only 15 met the criteria for inclusion in this review. Data from 14 trials provided evidence that TMS of the motor cortex, eliciting MEPs, is a reliable tool for predicting motor recovery as well as functional outcome. The interpretation of the results was complicated by methodological differences between the included studies.