Until very recently, Coxiella burnetii was viewed and studied as an obligate intracellular bacterium that relied exclusively on a eucaryotic host cell for growth. Other medically relevant obligate intracellular bacteria reside in the genera Anaplasma, Chlamydia, Ehrlichia, Orientia, and Rickettsia. An obligate intracellular lifestyle presents a significant obstacle to genetic transformation. Procedures that are straightforward with free-living bacteria, such as antibiotic selection and cloning, can be very difficult when growth of transformants is restricted to a host cell. Long-term passage in host cells to expand small transformant populations can further complicate the procedure. Despite these and other obstacles, at least rudimentary systems are currently available for genetic transformation of most obligate intracellular bacterial pathogens. Dramatically aiding the development of new genetic methods for C. burnetii is the recent discovery of a medium that supports host cell-free growth of the organism in liquid, and importantly, on solid media as clonal colonies. The expanded C. burnetii genetics toolbox now includes transposon systems for random mutagenesis and single-copy, site-specific chromosomal gene knock-ins, as well as a shuttle vector for heterologous gene expression and in trans complementation. A reliable method of targeted gene inactivation remains a challenge. Advances in C. burnetii genetic manipulation will allow identification of genes essential for intracellular parasitism and disease pathogenesis, and undoubtedly fuel new interest in this minimally studied bacterial pathogen.