In recent years, high dose chemotherapy followed by bone marrow rescue has been established as a common treatment of hematologic and solid tumor malignancies. Despite unequivocal success, relapse after transplant remains a serious problem, being the main cause of treatment failure. In an attempt to reduce relapse rates, we intensified the conditioning regimens consisting of busulfan/cyclophosphamide versus fractionated total body irradiation (f-TBI)/ cyclophosphamide by the addition of high dose etoposide. Toxicity profiles of 25 pediatric patients with hematologic malignancies undergoing intensified conditioning did not differ significantly between the two groups, except for a higher incidence of veno-occlusive disease in busulfan-treated patients (3 of 13 patients) compared with the TBI group (0 of 12 patients). We observed no transplant-related mortality in neither group. Regimen-associated morbidity was moderate and reversible in all cases. Five patients died in each treatment arm, due to relapse of the underlying disease. We conclude that both regimens are feasible in marrow transplantation of pediatric patients. Open randomized trials are needed to assess the efficacy of intensified conditioning in terms of disease-free survival.