In multiple system atrophy (MSA), sleep-related breathing disorders are commonly observed, including vocal cord abductor paralysis (VCAP), which can cause sudden death. In its early stage, VCAP occurs only during sleep, but as the disease progresses, it appears when both awake and asleep. We encountered a 59-year-old obese woman who had been under continuous positive airway pressure (CPAP) therapy for obstructive sleep apnea syndrome (OSAS) for approximately one year but later developed acute respiratory failure because of VCAP. VCAP was the predominant finding that led to the diagnosis of MSA in our patient. On laryngoscopic examination, the movement of the patient's larynx was normal during wakefulness, but VCAP, paradoxical movements of the vocal cord and a floppy arytenoid were observed during drug-induced sleep. We suggest that detection of VCAP and laryngopharyngeal abnormalities such as floppy arytenoid in the early stage of MSA is important for determining treatment options.