Lipopolysaccharides of Coxiella burnetii phase I and II were comparatively investigated by chemical and immunochemical methods. LPS of phase I (LPS I) and phase II cells (LPS II) show no serological cross reaction, indicating that the serological determinants of LPS II are masked in LPS I. Chemical analysis of LPS I and II show that phase I and II cells can be considered as S and R forms of Coxiella burnetii. The structure of LPS II has recently been elucidated and shows a dimannosylated core of an alpha(1,3)-linked heptose-disaccharide which is attached to a "KDO-like" substance. In enterobacterial core-types, alpha(1,3)-linked heptose-disaccharide is also part of the inner core structure, although the heptose occurring in enterobacterial R cores is the L-glycero-D-manno-heptose. In Coxiella burnetii we have only the rare D-glycero-D-manno-heptose which is the biosynthetic precursor of the former and is in many enteric LPS, present only in addition to L-glycero-D-mannoheptose. In these R-cores, it is occupying mostly terminal positions (Radziejewska-Lebrecht et al., 1981) and is absent from the main chain. The complete structure of LPS I is not yet available, but some important points could recently be clarified. The immunodominant sugars in LPS I are C-3-branched sugars, 6-deoxy-3-C-methyl-L-gulose (L-virenose) and 3-C-(hydroxymethyl)-L-lyxose (dihydro-hydroxy-L-streptose). These two sugars have not been found so far in other lipopolysaccharides and the latter one not previously in any other natural product. Their identification is based on GLC-MS comparison with authentic and synthetic compounds. Both branched sugars (and in addition part of the mannose) are the terminal sugars in LPS I. Sites of attachment of phase I-specific sugars to the LPS II-core are: the 3-position of a branched heptose and, presumably, the 4-position of a terminal D-mannose. The extreme acid-lability of the linkages of both branched sugars was investigated in detail and is caused by the nature of the branched sugars (deoxyhexose with bulky axial substituents; pentofuranose with axial OH-groups). No information is so far available on the (penultimate) sugars to which the branched sugars are linked, but methylation analyses with LPS I, and with the recently described I/CR mutant, which is selectively lacking the virenopyranose, are presently performed.