During the phase variation of Coxiella burnetii, modifications in its lipopolysaccharide (LPS) component were investigated. The cloned phase I C. burnetii cells were passed serially in chicken embryo yolk sacs up to the egg passage (EP) 90. The LPSs from the cells in EPs 3, 12, 21, 40, 60, and 90 were all separated by steric exclusion chromatography into three major populations: the high, intermediate, and low molecular weight fractions, differing one from another in size and chemical composition. No noticeable shortening of the O-polysaccharide chains was observed in the LPSs isolated during the C. burnetii cultivation. However, a redistribution of the existing LPS populations has been observed due to an increasing prevalence of those cells in the whole cell population that express LPS molecules with truncated O-chains and those being of R-type. In the high and intermediate molecular weight LPS populations, virenose and dihydrohydroxystreptose are lost gradually with the progress in phase variation. This occurs more readily with the former sugar. At present, the molecular mechanisms influencing the LPS modifications during the C. burnetii phase variation remain unclear.