In vitro studies have been essential to describe the molecular details of bacteria-host cell interactions in general and the functions of bacterial effector proteins in particular. Recent advancements in in vivo imaging techniques are facilitating the next logical step to visualize the dynamic infection process as it happens within the living host while analyzing the role of bacterial effector proteins in vivo. Data obtained from this emerging field of 'tissue microbiology', combined with the massive knowledge base generated from research in 'cellular microbiology' will eventually provide a complete picture of the complex infection process.