The obligate intracellular bacterium Coxiella burnetii is the etiological agent of acute Q-fever and chronic endocarditis in humans and of several zoonotic infections. The DNA from a variety of these disease isolates was compared for homology to the plasmid QpHl, found in the Nine Mile strain. Three patterns of homology were found in these isolates, i.e., one pattern identical to that of QpHl, one common to several endocarditis isolates and goat abortion isolates, and one common to the remaining group of endocarditis isolates. Plasmid DNA from the endocarditis-abortion isolate group, designated QpRS, was mapped by restriction enzyme analysis and compared with QpHl. These data show that QpRS was 2 to 3 kilobase pairs larger, contained DNA not found in QpHl, but was not generated from QpHl by a single insertional event. Isolation of plasmid DNA from the second endocarditis group of isolates was not successful and may indicate that the plasmid has integrated into the chromosome. This analysis provides the first clear evidence that differences exist between C. burnetii isolates which cause various diseases, indicating that different C. burnetii strains may have unique virulence characteristics. Coxiella burnetii is an obligate intracellular parasite that causes Q-fever (2). The disease normally presents as an acute febrile illness, with recovery occurring in 1 to 4 weeks. C. burnetii has also been implicated as the etiological agent in a number of cases of chronic endocarditis in humans. These infections have been considered to be due to the compromised nature of the host during infection and not to a specific property of the pathogen (6, 7, 11). C. burnetii is also a zoonotic pathogen, most notably responsible for late-term abortions in several domestic animals (e.g., goat and sheep; 1, 9). Comparative analyses of organisms isolated from hosts for each of these diseases have not indicated that there are any specific C. burnetii variants able to cause a particular