Motor evoked potentials (MEPs) are widely used in various neurological diseases, but have not been systematically employed in neurocritical care patients. We evaluated the clinical and predictive value of MEPs by magnetic transcranial stimulation in intensive care patients with acute brainstem lesions of predominantly vascular origin. In a prospective trial, a total of 30 patients with acute brainstem lesions were studied. Diagnoses were brainstem infarction (n=15), brainstem hemorrhage (n=3), encephalitis (n=1), basilar artery aneurysm (n=1), and space-occupying cerebellar infarct (n=5), cerebellar hemorrhage (n=3), and brainstem contusion (n=2). We performed MEP tests by transcranial stimulation to the abductor pollicis brevis bilaterally, bilateral somatosensory (SEPs) and auditory evoked (BAEPs) potentials. We determined motor function at the time of electrophysiological testing and after 3 months, the presence of radiologically confirmed lesions, and clinical outcome after 3 months. At the time of MEP recordings, ten patients were comatose, twelve stuporous, seven somnolent and one awake. MEPs were present bilaterally in seventeen, absent unilaterally in eight and bilateral absent in five patients. Absent MEP highly correlated with the presence of persisting motor deficit 3 months later (P<0.0001). Absent MEPs predicted motor deficit after 3 months with a high specificity and more precisely than the clinical examination at the time of MEP testing. MEP findings correlated with the presence of radiologically confirmed lesions within the brainstem (P<0.0001). Combined with SEP and BAEP data, MEPs predicted the presence of unilateral brainstem lesions with high accuracy. MEP recordings can be safely performed in neurointensive care patients and yield utilizable results. In patients with brainstem lesions, MEPs correlate with radiological findings and predict final motor function more accurately than clinical findings. MEPs are a reliable diagnostic tool for assessing motor function in otherwise unresponsive patients.