The prevalence of congenital heart diseases (CHDs) was estimated to be 8-12 per 1000 live births. Around 77.8% and 87.2% of cyanotic and asyanotic CHD cases experienced decrease in iron levels in the blood respectively. Anemia in children with CHDs, especially with cyanosis and high hematocrit levels due to chronic hypoxia, were often underdiagnosed. The Mentzer index as a diagnostic tool for anemia was used to diagnose iron deficiency in children with cyanotic and acyanotic CHDs. This research was a cross-sectional study done in Haji Adam Malik hospital by using data from medical records. Among 110 samples, TOF and VSD were diagnosed the most in cyanotic and acyanotic CHDs respectively in children aged 1 ? 5 years old. Hematological parameters such as hemoglobin, hematocrit and erythrocyte showed significant value (p<0.05) statistically. The difference of the Mentzer index with Mann-Whitney test showed significant difference (p<0.05) with median value of 12.0?3.9 and 17.2 ?4.2 in cyanotic and acyanotic CHD respectively.