Transcranial magnetic cortical stimulation provides the clinical neurophysiologist with a method to examine alterations in the function of central motor pathways in diseases affecting the motor system. The technique has great research potential and has led to increased understanding of intracortical physiology, corticospinal tract function, motor system plasticity and motor control. Subclinical cerebral and spinal cord lesions may be demonstrated, and the technique has a potential role for quantification and monitoring of disease progression, and for early prognostication after stroke. Intraoperative monitoring of motor evoked potentials (MEP) is of value during spinal cord surgery, but due to attenuation of magnetic MEPs during anaesthesia, transcranial electrical stimulation is more appropriate for intraoperative recordings.