Autologous recovery is a major problem with busulfan as a marrow ablative agent in conditioning children for allogeneic BMT. Data suggest the average concentration of busulfan at steady state (Bu Css) is critical for successful engraftment. We prospectively evaluated busulfan pharmacokinetics in 31 children (age 0.6-18 years) with AML (n = 9), and non-malignant diseases (n = 22) receiving HLA-closely matched (sibling, parent, unrelated) donor grafts. Blood samples were obtained following dose 1 and 13 of a standard 16 dose, 4-day regimen. The busulfan dose varied from 14 to 20 mg/kg. Patients received cyclophosphamide 200-240 mg/kg; 22/31 received 80-90 mg/kg of ATG. Eight patients failed to engraft (26%). ATG did not appear to influence engraftment (P = 0.38). Bu Css levels <600 ng/ml correlated with autologous recovery/mixed chimerism (P = 0.018). There were no graft failures in patients with a Bu Css >600 ng/ml. A correlation between Bu Css levels and regimen-related toxicity (RRT) was not identified for grade 2 or higher toxicities, only 1/31 had a Bu Css >900 ng/ml. Our data support the use of pharmacokinetic monitoring of busulfan.