ABSTRACT Background Multiple System Atrophy (MSA) dysphagia is routinely assessed by the Unified Multiple System Atrophy Rating Scale (UMSARS) part I‐item 2. Objective To compare the UMSARS part I‐item 2 with an ear/nose/throat (ENT) expert physician assessment. Methods We retrospectively analyzed the data of MSA patients who underwent an ENT assessment (nasofibroscopic and radioscopic exam) and an annual UMSARS assessment. Deglutition Handicap Index (DHI) and pulmonary/nutrition complications were collected. Results Seventy‐five MSA patients were included. The ENT assessment revealed more severe dysphagia compared to the UMSARS part I‐item 2 score (P = 0.003). A higher proportion of patients with impaired protective mechanisms showed severe UMSARS‐based dysphagia (P = 0.005). Patients with choking and oral/pharyngeal transit defects and nutritional complications were equally distributed across UMSARS part I‐item 2 scores. Worse UMSARS part I‐item 2 scores had worse DHI scores. Conclusions The UMSARS‐based assessment of dysphagia does not capture key aspects of pharyngo‐laryngeal dysfunction reflecting swallowing efficiency.