Transcranial magnetic stimulation with a conditioning-test paradigm was used to assess cortico-cortical interactions in the motor cortex of 11 patients with Huntington's disease (HD) as compared to normal controls (NC). In the HD patients, threshold and amplitude of motor potentials evoked in the opponens pollicis muscle at rest were not significantly different from NC. The cortico-cortical inhibition at interstimulus intervals of 2–5 ms was significantly reduced and the cortico-cortical facilitation at longer intervals (10–25 ms) was significantly enhanced. Changes of intracortical inhibition and facilitation were related to clinical rating of choreic dyskinesias. The data support the hypothesis of a functional impairment of the motor cortex-basal ganglia loop in HD patients.