This study is investigating children with congenital heart diseases, both cyanotic and acyanotic in term of apoptosis. DNA fragmentation, and antioxidant enzymes including : superoxide dismutase , catalase, and glutathione peroxidase . Also the study included the effect of medical laser : Helium-Neone (He-Ne), on the previous oxidative stress parameters on children with CHD . This study was carried out on two groups of patients with congenital heart diseases both cyanotic and acyanotic cases attending the cardiac unit and compared to normal healthy control group. Also there were two more groups of cyanotic and acyanotic cases, attending the cardiac catheterization unit, were examined after 24 hours post cardiac catheterization, and were exposed to medical laser irradiation and were also compared to another normal healthy control group. The final study population was 36 males and 36 females versus 18 males and 18 females as control group. In those groups, we investigated markers of oxidative stress in congenital heart diseases in terms of lipid peroxidation, apoptosis, DNA fragmentation and antioxidant enzymes including superoxide dismutase, catalase and glutathione peroxidase. Results indicated that there were significant increase in mean ± SD of plasma MDA, DNA fragmentation and apoptosis in circulating lymphocytes of cyanotic and acyanotic cases compared to controls. There was also no significant difference in the three mentioned parameters when both of them were compared with each other. There were no significant differences in antioxidant enzymes in all groups indicating that the body in congenital heart diseases adapts itself by increasing endogenous antioxidant enzymes. Laser ameliorated oxidative stress in controls and acyanotic heart disease blood post cardiac catheterization, but increased apoptosis and DNA fragmentation in cyanotic cases 24 hours post laser irradiation. Also, there was significant increase in plasma nitrite in controls, cyanotic and acyanotic cases 24 hours post irradiation with laser compared to their level without laser irradiation. However, cyanotic cases showed the highest significant value that was significantly higher when compared to both acyanotic and controls. Cyanotic and acyanotic congenital heart diseases have an altered balance of oxidative stress and increase in free radical generation as measured in terms of plasma malondialdehyde and DNA fragmentation.The body of congenital heart disease seems to adapt itself to the oxidative stress induced by chronic hypoxia by normalizing its levels of endogenous antioxidant enzymes and inducing apoptosis. He-Ne laser have an ameliorative effect on damaging effects induced due cardiac catheterization procedure in case of acyanotic congenital heart diseases, but it worsen the effects in cyanotic congenital heart diseases.Increased nitric oxide production seems to be the reason for the increased oxidative stress in cyanotic heart diseases, which are worsened when exposed to laser irradiation.