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A subset of aged individuals with Down syndrome (DS) exhibits eating, drinking, and swallowing (EDS) difficulties, which have the potential to lead to life-threatening conditions such as malnutrition. We report a case of 37-year-old woman with DS, who developed Wernicke’s encephalopathy related to malnutrition that was caused by EDS problems. The patient presented with a history of EDS problems for 2 years without treatment and had developed mental-status changes, unsteadiness of stance and gait with associated MRI findings, corresponding to Wernicke’s encephalopathy. The patient was treated with nutritional support including thiamine replacement and dysphagia rehabilitation therapy. Our case highlights the importance of early and proper management of malnutrition associated with EDS problems in adult DS. The suspicion of Wernicke’s encephalopathy must be considered when adult DS manifests as prolonged malnutrition, altered mentality and decreased mobility.