Malnutrition occurs when nutrient intake does not meet the needs for normal body functions and as a consequence leads to alterations of growth and development in children. Chronic illness puts children at risk for developing malnutrition. Because of children's rapid periods of growth and development, early diagnosis, prevention, and management of malnutrition are paramount. The reasons for malnutrition in children with chronic disease are multifactorial and are related to the underlying disease and nonillness-associated factors. This review addresses the causes, evaluation, and management of malnutrition in pediatric congenital heart disease, chronic kidney disease, liver disease, and cystic fibrosis. (Nutr Clin Pract. 2019;34:349-358)