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As the overall long-term event-free survival rate in children with acute lymphoblastic leukemia approaches 80%, emphasis is being placed on risk-directed therapy so that patients are neither overtreated nor undertreated. It has become apparent that a risk assignment system based on primary genetic abnormalities is inadequate by itself. For example, leukemias with the MLL-AF4 or BCR-ABL fusion gene are, in fact, heterogeneous diseases. Many require allogeneic hematopoietic stem-cell transplantation; some, if the patient is of favorable age and has a low presenting leukocyte count, can be cured with chemotherapy alone. Measurement of early responses to therapy and extent of minimal residual disease can greatly improve the accuracy of risk assessment. Consideration of the variable effects of therapy on the prognostic significance of specific genetic abnormalities is also important. Therefore, TEL-AML1 fusion confers a favorable prognosis in some protocols of chemotherapy but not in others. Studies to identify genetic polymorphisms with pharmacokinetic and pharmacodynamic significance promise to guide further refinement of treatment strategies. This will allow maximization of anticancer effects without induction of unacceptable toxicity in individual patients.