The bacterial type III secretion system is used by pathogenic Gram-negative bacteria to transfer toxin proteins directly into the cytoplasm of eukaryotic hosts. Pathogenic E. coli species including EPEC, EHEC and Shigella spp. use specialized T3SSs to deliver effector proteins into their mammalian hosts in order to manipulate the host response in their favor. Central to the T3SS is the injectisome, a syringe-shaped molecular nanomachine that spans both bacterial membranes and host cell membrane, providing a continuous channel from the bacterial to host cytoplasm. The last 5 years have witnessed significant progress in our understanding of the structure of the injectisome and the pathways that regulate its assembly and secretion. In this chapter, we will discuss these advances, focusing on the T3SSs of E. coli spp. including Shigella. We will first give an overview of the structural architecture of the injectisome and then discuss the mechanisms that regulate both its assembly and secretion.