A 27-year-old man with Behçet's disease presented with dyskinesia of the right hand and leg, but without paresis. MRI showed a discrete lesion in the internal segment of the left globus pallidus. SPECT (single photon emission tomography) disclosed increased perfusion in the hand and leg area of the left motor cortex and ipsilateral thalamus compared to that of the corresponding regions on the right. The dyskinesia was considered to be produced by disinhibition of the motor cortex due to loss of inhibitory inputs from the ipsilateral pallidum via the thalamus. Double transcranial magnetic stimulation revealed loss of suppression (loss of intracortical inhibition) of the left motor cortex while it showed normal suppression on the right, even though conventional techniques of magnetic stimulation failed to show any changes in excitability of the left motor cortex. We conclude that it is possible to detect changes of motor cortical excitability caused by dysfunction of some inputs from the basal ganglia by using the double cortical stimulation technique here described.