We have used transcranial magnetic stimulation of the motor cortex interictally in 12 patients with unilateral classic migraine with sensorimotor auras and 10 patients with common migraine and unilateral headache. In classic migraine, the threshold of activation of the FDI muscle by the cortical stimulus was significantly increased on the side of the auras, when compared to the unaffected side (P less than 0.01) and to normal subjects (P less than 0.01). The amplitude of EMG responses was also reduced in FDI on the affected side when compared to normals (P less than 0.02). Responses obtained in common migraine patients were normal on both sides. We suggest that some permanent subclinical dysfunction of the motor cortex might play a role in the pathogenesis of attacks of classic migraine with sensorimotor auras.