DNA microarrays enable the transcript levels of an entire genome to be measured simultaneously. Recent improvements in array manufacture, sample preparation, and data analysis are shifting emphasis from the technology itself to experimental design and the broader range of biological questions that can be addressed. The past year has also seen a transition from experiments involving a small number of conditions, with an emphasis on the specific genes induced or repressed, to experiments involving hundreds of conditions in which patterns of global gene expression are used to classify disease specimens and discover gene functions and drug targets. Basic research, medicine, and pharmacology are all likely to benefit from these advances.