Background: Children with congenital heart disease (CHD) are prone to malnutrition. Children with cyanotic CHD [CCHD] are specifically affected due to chronic hypoxia and iron deficiency anemia which is overlooked by pediatrician. This can have a significant effect on the outcome of surgery. Our objective was to determine the burden and determinant of malnutrition in children with several types of cyanotic congenital heart disease (CCHD).Methods: This case-control study included 80 children with symptomatic CCHD, and 40 healthy children matched for age and sex as a control group. Clinical evaluation and laboratory assessment of nutritional status were documented. Anthropometric measurements were recorded and Z scores for weight for age (WAZ), weight for height (WHZ), and height for age (HAZ) have been calculated. Haemoglobin, red cell indices and serum iron, total iron binding capacity and serum ferritin was done in cases and controls.Results: The overall prevalence of malnutrition was 72.5% in patients with CCHD and 22.5% in controls. Severe malnutrition was diagnosed in 68.9% of cases. All anthropometric measurements which markers of nutritional state are were significantly lower in the patients group compared to controls. The prevalence of iron deficiency anemia (IDA) was 47.5% in the study population. The study also showed that hemoglobin and hematocrit levels, RBC count were paradoxically higher in the cyanotic CHD as compared to the healthy controls though the iron studies revealed the iron deficiency. The mean corpuscular volume (MCV), mean corpuscular hemoglobin (MCH) mean corpuscular hemoglobin concentration (MCHC), serum ferritin, serum iron, total iron binding capacity (TIBC), values were the parameters, which were found to be statistically significant to differentiate the study groups.Conclusions: Malnutrition is a very common problem in children with symptomatic CCHD, the prevalence of IDA in children with CCHD was found to be high.