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Objectives: Cyanotic congenital heart disease (CCHD) predisposes patients to iron deficiency due to compensatory secondary erythrocytosis. This study aimed to determine the serum iron status and prevalence of iron deficiency among children with cyanotic congenital heart disease attending the Paediatric Cardiology outpatient clinic of Lagos State University Teaching Hospital, Lagos, Nigeria. Methods: This cross-sectional casecontrol study took place between May and October 2015 at the Lagos State University Teaching Hospital. A total of 75 children with cyanotic congenital heart disease and 75 apparently healthy age-, gender- and socioeconomicallymatched controls were analysed to determine serum iron status and the prevalence of iron deficiency as defined by the World Health Organization criteria. Results: The mean age of the children was 47.5 ± 2.9 months (range: 6–144 months old). Iron deficiency was significantly more frequent among CCHD patients compared to control subjects (9.3% versus 0%; P = 0.006). While latent iron deficiency was more prevalent among children in the control group compared to those with CCHD, this difference was not statistically significant (13.3% versus 9.3%; P = 0.303). No cases of iron deficiency anaemia were observed in the studied sample. Conclusion: Neither the children in the control group nor those with CCHD had iron deficiency anaemia. However, iron deficiency was significantly more prevalent among children with CCHD in Lagos. Periodic serum iron status screening is therefore recommended for this population.