Microarrays are a promising technique for elucidating and interpreting the mechanistic roles of genes in the pathogenesis of infectious disease. Microarrays have been used to analyse the genetic polymorphisms of specific loci associated with resistance to antimicrobial agents, to explore the distribution of genes among isolates from the same and similar species, to understand the evolutionary relationship between closely related species and to integrate the clinical and genomic data. This technique has also been used to study host–pathogen interactions, mainly by identifying genes from pathogens that may be involved in pathogenicity and by surveying the scope of the host response to infection. The RNA expression profile of pathogens has been used to identify regulatory mechanisms that ensure gene expression in the appropriate environment, to hypothesize functions of hundreds of uncharacterized genes and to identify virulence genes that promote colonization or tissue damage. This information also has the potential to identify targets for drug design. Furthermore, microarrays have been used to investigate the mechanism of drug action and to delineate and predict adverse effects of new drugs. In this paper, we review the use of spotted and high-density oligonucleotide arrays to study the genetic polymorphisms of pathogens, host–pathogen interactions and whole-genome expression profiles of pathogens, as well as their use for drug discovery.