We investigated 100 patients with a one-sided, functionally relevant hemiparesis after stroke. Motor evoked potentials (MEPs) were obtained from the anterior tibial muscle four or more weeks after the insult as well as after an eight week period of inpatient rehabilitation. The MEP results were correlated with motor deficit, walking ability, and activities of daily living (ADLs). Patients with loss of MEP had lower scores on the Motricity Index (MI) both at the beginning and at the end of the rehabilitative treatment (p < 0.001) and also gained fewer points on the MI than patients with preserved MEP. This was the case even when analyzing the lower limb scores alone (p < 0.001 before treatment, p = 0.003 after eight week rehabilitation). When the MEP was preserved, patients were more likely to regain independence in walking (specificity 0.67, positive predictive value 0.96) and stair climbing (specificity 1.0, positive predictive value 1.0). Patients with preserved MEP also scored higher on global outcome scales such as Barthel Index (BI), Functional Independence Measure (FIM) and Glasgow Outcome Scale (GOS). However, these differences did not reach statistical significance (p > 0.05). According to our results, MEPs of the lower extremity are of predictive value for the rehabilitative treatment of patients in the postacute phase after stroke. This is especially true for the extent of the motor impairment and walking ability. The utilization of MEPs for prediction of future levels of disability and handicap is limited and only useful taking into consideration other clinical and diagnostic findings as well as the patients' cognitive, emotional and social state.