Objective: To establish the prevalence of iron deficiency among children with cyanotic heart disease. Design: Cross-sectional study. Setting: The study was carried out at Kenyatta National Hospital and Mater Hospital from August to December of 2007. A total of 112 children meeting the eligibility criteria were recruited from the wards and the cardiac clinics. Subjects: These were children less than 18 years of age, with cyanotic heart disease confirmed on ECHO, presenting at the paediatric cardiac clinic of the two hospitals or admitted in the wards at Kenyatta National Hospital. These were patients who had not undergone surgical correction. Results: The prevalence of iron deficiency was found to be 16.9% (95% CI 9.8- 24.1%). Conclusion: There is a high prevalence of iron deficiency among patients with congenital heart disease with cyanosis in the two institutions. Routine screening for iron deficiency is recommended for these children and those found to be deficient should be treated.