Magnetic stimulation of the motor cortex is of value in the diagnosis and management of several neurological disorders. Marked latency prolongation is suggestive of demyelination of central motor pathways, whereas low-amplitude responses with little delay are more typical of disorders causing neuronal loss or axonal degeneration. Subclinical abnormalities may be demonstrated, and the technique has a potential role for quantification and monitoring of disease progress. The pattern of early electrophysiological abnormality is of prognostic value in stroke patients.