Background & objectives: Oxidative stress can cause many diseases and increases the risk of post-operative complications in children with congenital heart disease. For these reasons, this study was aimed to investigate the differences between cyanotic and acyanotic paediatric patients who underwent heart surgery with markers of oxidative stress. Methods: Eighty five patients were included in the study. The samples taken before the surgery and within the first 24 h after the surgery were evaluated for haemoglobin (Hb), leukocytes, uric acid, glutathione (GSH), malondialdehyde and total antioxidant capacity. Cyanotic, acyanotic, hyperoxygenated, normo-oxygenated, cardiac surgery with or without cardiopulmonary bypass (CPB) comparisons were made. Results: Positive correlation was found between age and pre-operative total antioxidant status values. Cyanotic and acyanotic patients did not have different antioxidant reserve capacities preoperatively. Although pre-operative thiobarbituric acid reactive substances (TBARS) levels were significantly lower in cyanotic patients, post-operative levels were higher. TBARS levels increased and GSH levels reduced postoperatively. The level of oxygenation did not cause a significant difference on markers of oxidative stress. The duration of CPB did not have negative effects on oxidative stress. Interpretation & conclusions: Cyanotic and younger patients were found to be more vulnerable to oxidative stress. The increased levels of TBARS and the decreased levels of GSH could be the indicators of oxidative damage depending on many factors such as surgery, CPB, ischaemia/reperfusion, inflammation, iron overload and oxygenation. The level of oxygenation does not cause a noticeable difference in oxidative stress. CPB causes oxidative stress, but if it is conducted appropriately, the duration of CPB does not cause a significant negative impact on oxidative stress.