The efficacy of current treatment protocols for childhood cancer is mainly based on empirical studies by adding drugs, changing drug dosages and changing drug combinations. In pediatric acute lymphoblastic leukemia (ALL), this approach has resulted into approximately 80% 5-year disease-free survival whereas less favorable results have yet been obtained for acute myeloid leukemia (AML), i.e. approximately 50%, and other types of tumors, e.g. approximately 60% for medulloblastoma. A further optimization of therapy results requires more insights into the molecular biology of tumor cells, including genetic defects and aberrant expression of genes. This knowledge is needed to rationally develop more specific therapies in which relapse-risk and side-effects of therapy are reduced using targeted drugs. Genome-wide analysis of gene expression levels (mRNA) has revealed many new insights into the biology of leukemic cells. In this review we will discuss the recent progress that has been made in the use of microarrays for identifying new markers and targets for treatment of acute leukemia in children.