A central feature of type III protein secretion machines is their ability to engage their substrates in a hierarchical and organized fashion. The hierarchy in the secretion process is first observed during the assembly of the type III secretion injectisome when the secretion machine exclusively engages proteins required for building the needle complex substructure (early substrates). After completion of the needle complex, the secretion system loads the proteins that will form the needle tip substructure as well as the protein translocases (middle substrates), which upon contact with host cells will mediate the passage of effectors (late substrates) through the host plasma membrane. The hierarchy of the secretion process is orchestrated by a very large cytoplasmic complex known as the sorting platform, which selects and initiates the substrates into the secretion pathway.