The development, refinement and increasingly widespread use of DNA microarrays have been important responses to the explosion of sequence information produced by genome science. The high sample densities possible with DNA microarrays, coupled with the complete or nearly complete genome sequences available for humans and model organisms, provide a powerful analytical method to measure both qualitative and quantitative variations in RNA and DNA. Principal among the applications of microarrays is the large-scale analysis of RNA expression, often referred to as expression profiling. The power of this application lies in its ability to determine the expression patterns of tens of thousands of genes in a single experiment. Additionally, the ability to detect DNA polymorphisms makes microarrays useful in studies designed to correlate DNA sequence variations with variations in phenotype. The unprecedented scale on which microarrays allow both experimentation and generation of results should make possible a more complete and comprehensive understanding of cells and cellular processes.