Polysomnography, electromyography (EMG) of the face, tongue, and soft palate, blink reflexes (BRs), EMG during bottle-feeding, and brainstem auditory evoked responses (BAERs) were performed in 25 newborn babies with isolated Pierre Robin sequence (PRS) to aid in evaluation and management. Obstructive apneas were found in 23/24 patients (the 25th having undergone tracheotomy). Number and duration of central respiratory pauses were always normal, as well as electroencephalographic and clinical organization of sleep stages. EMG recruitment pattern in facial and lingual muscles, and BRs were normal in all cases. EMG recruitment pattern in muscles of the soft palate was normal in 14/25 patients, showed a reduced average amplitude with short-duration and low amplitude motor unit potentials in 10/25, and showed signs of denervation in 1/25. EMG during bottle-feeding showed sucking-swallowing disorders in 20/25 patients. BAERs showed a bilateral conductive impairment with increased latencies and thresholds in 5/19 patients, but with normal and symmetric I-III and I-V interpeak latencies in 19/19. These neurophysiological findings suggest that in isolated PRS a dysfunction of the lingual and pharyngeal motor organization exists without any structural impairment in brainstem nuclei and pathways.