A follow-up analysis of the prospective ALL-SCT-BFM-2003 trial and its subsequent extension registry confirmed a higher risk of subsequent malignant neoplasms (SMN) in children with acute lymphoblastic leukemia (ALL) receiving total body irradiation (TBI)-based conditioning for hematopoietic stem cell transplantation. In all, 558 patients >2 years of age received conditioning with TBI 12 Gy/etoposide and 110 children ≤2 years of age and those with contraindications for TBI received busulfan/cyclophosphamide/etoposide. The 5-year cumulative incidence of SMN was 0.02 ± 0.01, while the 10-year rate was 0.13 ± 0.03. Thirty-three patients, all in the TBI group, were diagnosed with a total of 39 SMN, including 34 solid tumors and five myelodysplastic syndromes/acute myeloid leukemia at a median of 5.8 years. Of those patients, 64% (21) were alive at a median 5.1 years after the diagnosis of their first SMN. The only significant risk factor for the development of SMN, based on univariate analysis, was TBI vs. non-TBI based conditioning. In the future, prospective, controlled studies are needed to evaluate other conditioning regimen approaches aimed at preventing subsequent development of SMN without negatively impacting overall leukemia-free survival.