Many bacterial pathogens utilize specialized secretion systems to deliver virulence factors into the extracellular milieu. These exported effectors act to manipulate various processes of targeted cells in order to create a suitable niche for bacterial growth. Currently, seven different types of secretion system have been described, of which Type I – VI are mainly present in Gram-negative bacteria and the newly discovered Type VII system seems exclusive to Gram-positive species. This review summaries our current understanding on the architecture and transport mechanisms of each secretion apparatus. We also discuss recent studies revealing the roles that these secretion systems and their substrates play in microbial pathogenesis.