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Six patients with alternating hemiplegia of childhood (AHC) underwent motor evoked potentials (MEPs), somatosensory evoked potentials (SEPs) and blink reflex recording. No SEP abnormality was found. As for MEP recording, central conduction time did not differ between patients studied during either interictal or ictal phase, and normal subjects, suggesting that the pyramidal system function is spared. In blink reflex recording, the latencies of both the ipsilateral (iR2) and contralateral (cR2) R2 components were significantly longer (P < 0.01) in patients during the interictal phase than in normal subjects. Moreover, the iR2 and cR2 areas were significantly reduced (P < 0.01) in patients during the interictal phase, compared with normal subjects. During the ictal phase, the ipsilateral R2 latency was significantly decreased after stimulation of the hemiplegic side, compared with the interictal phase (P < 0.05). The blink reflex abnormalities suggest a brainstem dysfunction, which may be linked to the pathophysiological mechanisms of the disease.