Conditioning regimens preceding hematopoietic SCT (HSCT) usually consist of high-dose chemotherapy. Chemotherapy and radiation therapy are associated with increased formation of free radicals and depletion of critical plasma and tissue antioxidants. Oxidative stress and antioxidant depletion have been described during the transplantation period in HSCT patients. In a limited number of studies, it was observed that the conditioning regimen resulted in oxidative stress and antioxidant depletion in HSCT patients. The objective of this study was to look for further evidence of oxidative stress and antioxidant status in pediatric HSCT patients. In this study, blood samples were collected from 21 pediatric allo-HSCT patients before and after conditioning therapy. Erythrocyte and plasma malondialdehyde (MDA) levels, erythrocyte reduced and oxidized glutathione (GSH) levels, erythrocyte antioxidant enzymes activities, plasma α-tocopherol and β-carotene levels were determined. After high-dose chemotherapy, erythrocyte and plasma MDA levels increased. Reduced GSH levels decreased whereas oxidized GSH levels increased first and then decreased significantly compared with the values before the chemotherapy regimen. It was also observed that catalase, superoxide dismutase and GSH-S-transferase activities decreased, but there was no change in GSH peroxidase activity. On the other hand, plasma α-tocopherol levels increased, but β-carotene levels did not change.