Background: Some elements were claimed to play a role in the pathogenesis of congenital heart defects (CHD) and influence the general well-being and health of these children. Objectives: We aimed to assess the levels of some elements simultaneously in the blood and teeth samples of children with cyanotic and acyanotic CHD compared with healthy children. Methods: A total of 39 children with CHD (11 with cyanotic and 28 with acyanotic CHD) and 42 age- and sex-adjusted controls were enrolled. Levels of 13 elements, including magnesium, phosphorus, calcium, chromium, manganese, iron, copper, zinc, strontium, cadmium, lead, mercury, and molybdenum, were assessed using inductively coupled plasma mass spectrometry. Results: Children with cyanotic and acyanotic CHD had significantly lower teeth calcium and calcium/phosphorus ratio as compared to the controls after adjusting for confounders. The mean blood iron level was found to be significantly higher in the cyanotic CHD group compared to the other groups. In addition, children with acyanotic CHD had significantly higher teeth copper levels, higher blood molybdenum and lower blood magnesium levels compared to the healthy control group. Blood cadmium and mercury levels were found to be significantly elevated in both the cyanotic and acyanotic CHD groups compared to the healthy control group. There were no differences in toxic metal levels of teeth in cases with CHD. Conclusion: Monitoring adequate and balanced gestational micronutrient intake might support not only maternal health but also fetal cardiac development and infant well-being. Supplementation of magnesium should be evaluated in patients having CHD.