Transcranial magnetic stimulation allows painless, non-invasive stimulation, neurophysiological evaluation of nervous structure covered by bone or difficult to access for other reasons. In the clinical setting the technique is mainly used for the investigation of the corticospinal tract (motor evoked potential: MEP). Based upon our experience with patients examined over the course of four years, we have attempted to highlight the clinical situations, where diagnostic help is provided by this technique. MEP in general has proved to be a sensitive and reliable examination. Its significance is apparent mainly in situations where clinical signs of corticospinal tract dysfunction are not evident, or they are masked by lower motoneurone involvement, and where neuroimaging techniques are not informative. The demonstration of subclinical corticospinal lesion is often essential to establish the diagnosis in multiple sclerosis and amyotrophic lateral sclerosis. The technique however received little attention so far with respect to its role in the diagnosis of various spinal cord disorders, and in the demonstration of intact corticospinal function in case of weakness, psychogenic in origin. We have endeavored to provide further evidence in support of this, and thereby advocating a wider clinical application of the technique.