Presence of specific chromosomal abnormalities is one of the most important prognostic factors in acute myeloid leukemia (AML). Recent advances in molecular biology have allowed structural and functional characterization of many of these genomic rearrangements. In many instances, AML is associated with gene fusion, whereby segments from two different genes fuse to give rise to a chimeric structure consisting of the 5' end of one gene and the 3' end of another. Recombinant DNA technology has also permitted the creation of animal models for in vivo studies of the leukemogenic role of several of these chimeric proteins. This review presents current information on the molecular biology and the clinical significance of three of the most common molecular subtypes of AML. In the first two, t(8;21)(q22;q22) and inv(16)(p13q22), disruption of genes encoding for subunits of core-binding factor (CBF), a transcriptional regulator of normal hematopoiesis, occurs, suggesting a common leukemogenic pathway. The third subgroup is characterized by disruption of MLL, a gene that is located at chromosome band 11q23 and encodes a putative transcriptional regulator. This gene is commonly involved in reciprocal translocations of chromosome 11q23 with other gene partners, but, in some instances, MLL disruption occurs by a mechanism of partial tandem duplication, in the absence of any other partner gene. Current data suggest that identification of specific genetic abnormalities in newly diagnosed AML patients is important to predict clinical outcome and, perhaps, to select different therapeutic strategies. The predictive value of detecting these molecular markers to predict cure or relapse in AML patients in complete remission following definitive treatment is still uncertain.