BACKGROUND: Children with severe motor and intellectual disabilities (SMID) are at a high risk of malnutrition and often require tube feeding to maintain their nutritional status. However, determining their energy requirements is difficult since inadequate dietary intake, severe neurological impairment, respiratory assistance, and cognitive impairment are all factors that affect malnutrition in SMID. AIM: This study investigated the factors affecting malnutrition and identified problems affecting the nutritional status of children with SMID. METHODS: Forty-two children with SMID with oral motor dysfunction who were receiving home medical care at one of four hospitals were enrolled. Their nutritional status was assessed using a 3-day dietary record, anthropometric measurements, and laboratory tests. The clinical findings associated with malnutrition were compared, and a body mass index (BMI) z-score less than -2SD was defined as malnutrition. The relationship between BMI z-score and other potential predictors was also investigated. RESULTS: Thirty-three (79%) children received tube feeding, and 20 (48%) experienced malnutrition. The median age of the malnourished children was older than that of non-malnourished children. Respiratory assistance was significantly correlated with higher BMI z-score, independent of other potential confounders such as nutrition method, muscle tonus, and energy intake. Cholesterol levels were significantly higher in children receiving a standard infant formula beyond 3 years of age than in those who switched to enteral formula before 3 years of age. CONCLUSIONS: Malnutrition in children with SMID was mainly associated with age or respiratory condition. Energy requirements should be regularly re-evaluated with considering these factors.