Proper nutritional management is important for the growth and development of children with motor or intellectual disabilities; however, few studies have investigated the nutrient intake of children with disabilities. This study aimed to investigate the nutrient intake and food groups that are the main sources of nutrients for children with disabilities. This cross-sectional observational study included twenty-five children (mean age, 11⋅8 years) from five hospitals in Japan. Using a 3-d weighed dietary record, we estimated the daily nutrient intake and food and beverage sources that contributed to nutrient intake. The mean values of calcium, magnesium, iron, vitamin A, thiamine, riboflavin, and vitamin C intake were below the recommended dietary allowance, and those of dietary fiber and potassium were below the levels recommended by the Tentative Dietary Goal for Preventing Lifestyle-related Diseases (DG). In contrast, the mean intake values of fat, saturated fatty acids, and sodium were above the DG levels. Dairy products, meat, vegetables, and cereals were found to be the major contributors of nutrients. Increased intake of vegetables may help alleviate insufficient micronutrient intake in children with disabilities.