Autotransporter proteins are virulence factors associated with a wide variety of diseases caused by pathogenic gram-negative bacteria, and they play a variety of roles in pathogenesis including disabling host defences and mediating colonization. Pertactin, a key component of the whooping cough vaccine, is an autotransporter protein. A large sub-family of the autotransporters carries a trypsin-like protease domain, but these enzymes have different substrates and functions. The unique export process which defines the autotransporter family involves the polypeptide chain C-terminus forming a barrel structure in the bacterial outer membrane, but the role of this barrel in secreting of the N-terminal 'passenger' domain remains very unclear. There are now four published crystal structures of passenger proteins or fragments of them. We have compared these models to catalogue common features and to help predict the structures and functions of other autotransporter proteins such as SepA, which is involved in the pathogenicity of Shigella.