We investigated primary motor cortex and brain stem plasticity in patients with Gilles de la Tourette syndrome. The study group comprised 12 patients with Gilles de la Tourette syndrome and 24 healthy subjects. Patients were clinically evaluated using the Yale Global Tic Severity Scale. We tested cortical plasticity by conditioning left primary motor cortex with intermittent or continuous theta-burst stimulation in 2 separate sessions. Test stimulation consisted of 20 motor-evoked potentials recorded from right first interosseous muscle before and after thetaburst stimulation. We also tested brain stem plasticity by conditioning the right supraorbital nerve with facilitatory electric high-frequency stimulation delivered at the same time as the late response of the blink reflex or inhibitory high-frequency stimulation delivered before the late response on 2 separate sessions. Test stimulation consisted of 10 blink reflexes from the right orbicularis oculi muscle before and after highfrequency stimulation. After intermittent theta-burst stimulation, motor-evoked potential amplitudes in healthy subjects increased significantly but remained unchanged in patients. Similarly, after continuous theta-burst stimulation, motor-evoked potential amplitudes decreased significantly in healthy subjects but did not in patients. After facilitatory high-frequency stimulation, the blink reflex late response area in healthy subjects increased, whereas after inhibitory high-frequency stimulation, it decreased. Conversely, in patients, both interventions left the blink reflex late response area unchanged. The lack of the expected inhibitory and facilitatory changes in motor-evoked potential amplitudes and blink reflex late response area suggests that abnormal plasticity in the primary motor cortex and brain stem play a role in the pathophysiology of Gilles de la Tourette syndrome.