Background: Malnutrition among children with Congenital Heart Disease (CHD) is considered a major public health problem causing significant impact on children morbidity and mortality. Objectives: The study aimed to assess the prevalence and epidemiological pattern of malnutrition among under-five Egyptian children with CHD. Methods: A cross sectional analytical study design included 300 children, having uncomplicated CHD. Hemoglobin level, serum iron and total iron binding capacity were recorded. Additionally, Anthropometric measurements were assessed and Z scores were calculated for weight for age (WAZ), weight for height (WHZ), and height for age (HAZ) have been calculated. Malnutrition was defined as weight, height, and weight/height Z score <–2. Results: Generally, prevalence of malnutrition among the studied sample of CHD children was 47%. Forty–four percent of the studied population were underweight, 29.7% were stunted, while wasting was only 6.7%.  Malnutrition was significantly higher among those with low income compared to their expenditure (P = 0.038) and was significantly lower in those breastfed on regular intervals compared to those fed on demand (P = 0.002). Additionally, malnutrition was significantly higher in those receiving complementary feeding compared to those breastfed or bottle fed only (P value 0.03).Conclusion: Malnutrition is an obvious complicating problem in children with CHD, associated with existence of anemia, breastfeeding on demand and early- starting of complementary feeding.