Trace elements are essential micronutrients for the human body. In this study, we evaluated the alterations in copper, chromium, manganese, selenium, magnesium, zinc, iron, arsenic, boron, and silicon levels in children with cyanotic and acyanotic CHD who underwent cardiac surgery with cardiopulmonary bypass. Participants were divided into the following three groups: patients acyanotic CHDs (n=34), patients with cyanotic CHDs (n=30), and healthy controls (n=30). Blood samples were collected before the surgery and 1 hour after the sternum was closed. Serum trace elements were determined by Inductively Coupled Plasma Optical Emission Spectrometer-ICAP 6000. The baseline serum arsenic, manganese, and zinc levels of both patient groups were lower compared with controls, but there was no significant difference between baseline serum trace element levels of cyanotic and acyanotic patients. In both the patient groups, there was a significant decrease in postoperative serum arsenic, boron, copper, and zinc levels, and a significant increase in postoperative serum iron and magnesium levels. Silicon levels increased in cyanotic patients. Alterations in trace element levels were in the same direction in cyanotic and acyanotic patients. Copper, zinc, and manganase replacement may be needed after on-pump cardiac surgery.