Lipopolysaccharides (LPSs) extracted from nine strains of Coxiella burnetii were analyzed for chemical compositions, molecular heterogeneity by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and lethal toxicities in galactosamine-sensitized mice. The structure of a unique disaccharide of hydrolyzed phase I LPS was determined to be galactosaminuronyl-alpha (1-6)-glucosamine (GalNU-alpha (1-6)-GlcN, C12H22N2O10) with an Mr of 354. The Mr of LPSs of C. burnetii intra- and interspecific strains and the content of GalNU-alpha (1-6)-GlcN and two sugars, virenose and dihydrohydroxystreptose, were used as biochemical markers of truncated LPSs. Smooth-phase I LPS contained all three compounds, semi-rough-phase I LPS did not contain virenose, and rough-phase II LPS contained none of the three compounds. These analyses indicate that the intermediate to larger Mr LPSs require the addition of GalNU-alpha (1-6)-GlcN and dihydrohydroxystreptose to obtain the major (10.5 kDa), the intermediate (between 10.5 and 27 kDa), and the minor (23 kDa) LPS bands. The addition of virenose to the major and the minor bands produced the large Mr phase I LPSs. Extreme microheterogeneity in the banding profile ranging in Mr from the 2.5 to 10.5 kDa may be due to unidentified components, while the microheterogeneity in Mr of the 10.5-kDa and larger LPS bands is related to variations in the compounds described here. All of the LPSs were toxic in galactosamine-sensitized mice, albeit they were 100-1000-fold less toxic than Escherichia coli and Salmonella typhimurium endotoxin.