Despite differences in disease pathologies and host range, many enteric pathogens, including Salmonella and Shigella spp., utilize a remarkably similar machinery to secrete proteins that promote their entry into host cells. Analogous structures are required for the export of virulence proteins in other animal and plant pathogens. While the structure and organization of the gene complexes specifying these secretory pathways are broadly conserved, their phylogenetic distribution and genomic locations suggest that these sequences arose independently in divergent pathogens.