Tremendous progress has been made recently in research in the field of microbial pathogenesis and especially in the subfield of cellular microbiology. For instance, there has been significant development in research involving well-known microorganisms such as Salmonella. However, this issue of Current Opinion in Microbiology deliberately ignores these well-known microorganisms in order to focus on microorganisms that may be less well understood, but for which a significant impact is expected from genomics. All the reviews appearing in this issue were written by experts with this in mind and, indeed, they show that genomics and proteomics will soon bring the state of understanding of the pathogenesis of these organisms up to that of Salmonella. In this overview, we shall provide a brief synopsis of the pathogens described in this issue, followed by a description of the areas in which genomics is expected to have a major impact.