Background: Cyanotic congenital heart disease (CCHD) predisposes patients to iron deficiency due to compensatory secondary erythrocytosis. Objective: This study aimed to assess the prevalence of iron deficiency among infants and children having cyanotic and non-cyanotic congenital heart disease. Patients and methods: This was a case-control study enrolled 30 children with congenital heart disease whether cyanotic or non-cyanotic at the Department of Pediatrics and Intensive Care Cardiology Unit, Faculty of Medicine at Zagazig University Pediatrics Hospital. They divided into 15 cyanotic and 15 non-cyanotic congenital heart disease. In addition, 15 healthy age- and sex-matched children were included as a control group ranged from 1 to 5 years ago. Children were investigated by doing complete blood count, pulse oximetry, erythrocyte indices and iron profile, based on the transferrin saturation. Results: Iron deficiency anemia was found among 7 (53.3%) patients with CCHD, 2 (13.3%) patients with non-cyanotic congenital heart disease and 5 (33.3%) healthy children. There was no statistically difference between CCHD children, non-cyanotic congenital heart disease children and normal healthy children. Conclusion: Iron deficiency anemia remains a very common health problem and leads to high morbidity and mortality rates among children with congenital heart disease.