As in many other areas of basic and applied biology, research in infectious diseases has been revolutionized by two recent developments in the field of genome biology: first, the sequencing of the human genome as well as that of many pathogen genomes; and second, the development of high-throughput technologies such as microarray technology, proteomics, and metabolomics. Microarray studies enable a deeper understanding of genetic evolution of pathogens and investigation of determinants of pathogenicity on a whole-genome scale. Host studies in turn permit an unprecedented holistic appreciation of the complexities of the host cell responses at the molecular level. In combination, host-pathogen studies allow global analysis of gene expression in the infecting bacterium as well as in the infected host cell during pathogenesis providing a comprehensive picture of the intricacies of pathogen-host interactions. This chapter briefly explains the principles underlying DNA microarrays including major points to consider when planning and analyzing microarray experiments and highlights in detail their practical application using the interaction of Neisseria meningitidis with endothelial cells as an example.