Background: Ineffectiveness of nutritional programs directed toward children with special care needs and studies on risk factors for malnutrition among those children in Iraq are absent although increased clinical reports of malnourished disabled children. This study aimed to find out the disability types associated with malnourishment in addition to identifying the disabled children characteristics related to malnutrition. Methods: Present study was a cross sectional study conducted in Nine Governmental Institutes in Baghdad city through the period from March 01, 2016 to November 30, 2016 on 413 children with disability of deafness, blindness, Down’s syndrome, and autism. Results: The anthropometric means were significantly higher among children with mental disability (p<0.001), especially among children with Down’s syndrome (p<0.001). Monthly income and educational status of children mothers were significantly risk factors of malnutrition of children with special care needs (p<0.001). Conclusion: Malnutrition of children with special care is commonly affected by type of disability.