Numerous bacterial proteins exert their function outside the prokaryotic cell. To this end, both Gram-negative and Gram-positive bacteria have evolved specialized mechanisms to transport their proteins to the bacterial supernatant or host cell cytoplasm, so called secretion systems. These different strategies will be briefly discussed, followed by an in depth description of the Type III secretion system, an efficient molecular syringe assisting Gram-negative bacteria in entrance, growth and survival in eukaryotic host cells. Topics addressed include classification and role of multiple Type III secretion systems, the mechanism of protein translocation into the host cell as well as substrate recognition and chaperoning. Chlamydiales have also been found to encode a Type III secretion system and associated effector proteins. In contrast to the genetic organization in other bacteria, the encoding genes are scattered throughout the genome. To date, no structural information is available on the chlamydial Type III secretion system. We therefore propose a model of the chlamydial Type III secretion system and summarize current knowledge on the role of Type III secretion in the different stages of the chlamydial developmental cycle.