Once considered to be contained, infectious diseases of bacterial origin are now making a comeback. A lack of innovative therapies and the appearance of drug-resistant pathogens are becoming increasingly serious problems. A better understanding of pathogen–host interactions at the cellular and molecular levels is necessary to define new targets in our fight against microorganisms. In the past few years, the merging of cell biology and microbiology has started to yield critical and often surprising new information on the interactions that occur between various pathogens and their mammalian host cells. Here we focus on the intracellular routing of vacuoles containing microorganisms, as well as on the bacterial effectors and their host-cell targets that control vacuole maturation. We also describe new approaches for isolating microorganism-containing vacuoles and analysing their molecular composition, which will help researchers to define the molecules and mechanisms governing vacuole biogenesis.