Microarray-based techniques allow us to visualize and quantify the expression of every single gene in any population of cells. In yeast the true potential of large-scale transcriptome analysis in identifying regulatory units and understanding gene function has already been demonstrated by evaluating expression profiles of a comprehensive group of mutants. We discuss the potential of DNA-chip technologies for the analysis of gene expression in complex organisms. The usefulness of transcriptome analysis for clinical purposes und diagnosis of cancers is already well established. We argue that microarray-based expression profiling will also be a useful tool for the analysis of gene function and approaches complementary to classical phenotypic description in mammals, particularly in regard of the large resources of mutant models that are currently being generated by gene-targeting and mutagenesis of the mouse genome. Experimental requirements and potential future directions are discussed.