The ability of bacteria to transport proteins across their membranes is integral for interaction with their environment. Distinct families of secretion systems mediate bacterial protein secretion. The human pathogen, Coxiella burnetii encodes components of the Sec-dependent secretion pathway, an export system used for type IV pilus assembly, and a complete type IV secretion system. The type IVB secretion system in C. burnetii is functionally analogous to the Legionella pneumophila Dot/Icm secretion system. Both L. pneumophila and C. burnetii require the Dot/Icm apparatus for intracellular replication. The Dot/Icm secretion system facilitates the translocation of many bacterial effector proteins across the bacterial and vacuole membranes to enter the host cytoplasm where the effector proteins mediate their specific activities to manipulate a variety of host cell processes. Several studies have identified cohorts of C. burnetii Dot/Icm effector proteins that are predicted to be involved in modulation of host cell functions. This chapter focuses specifically on these secretion systems and the role they may play during C. burnetii replication in eukaryotic host cells.