With novel genome-wide technologies it is nowadays possible to perform detailed molecular analyses of normal and malignant tissues. Acute myeloid leukemia (AML) is a heterogeneous group of diseases with variable response to therapy. Gene expression profiling and genome-wide genotyping have recently been successfully applied to unravel the heterogeneity of AML. This chapter gives instructions and recommendations for genome-wide gene expression analyses, genotyping, and copy number analyses, as performed for AML using Affymetrix GeneChips.