S. aureus pathogens utilize multiple methods to invade mammalian hosts, damage tissue sites, and baffle the immune system from responding. Secretion of proteins across phospholipid membranes are one of the essential strategy components in these strategies for many bacterial pathogens. Secreted proteins play many roles in promoting bacterial virulence, from enhancing attachment to eukaryotic cells, to scavenging resources in an environmental niche, to directly intoxicating target cells and disrupting their functions. Many pathogens use dedicated protein secretion systems to secrete virulence factors from the cytosol of the host environment or bacteria into host cells. In general, bacterial protein secretion apparatuses are classified into classes, based on their structures, functions, and specificity. Some systems are conserved in all classes of bacteria and secrete a broad array of substrates, while others are only found in a small number of bacterial species and/or are specific to only one or a few proteins. In this chapter, we review the canonical features of several common bacterial protein secretion systems, as well as their roles in promoting the virulence of bacterial pathogens and immune-pathogenesis. Additionally, we address recent findings that indicate that the innate immune system of the host can detect and respond to the presence of protein secretion systems during mammalian infection.