The availability of whole-genome nucleotide sequence data from an ever-growing list of microbial genomes, including complete genomes for multiple strains within a species, presents an opportunity to overcome the challenges presented by antimicrobial drug resistance. The development of DNA microarrays provides a unique tool to understand pathogenic microbial genomes from a global perspective. Genome-wide expression profiles can facilitate the characterization both of the mechanisms of action and of the mechanisms of resistance to antimicrobial agents. Expression data have also been used to initiate the characterization of genes of unknown function, potentially leading to the identification of novel drug targets. Initial studies using DNA microarrays to analyse the host and pathogen responses to infection have also been performed, impacting our understanding of pathogenesis and the strategies taken to combat infectious diseases.