Recently novel Brucella strains have been reported with phenotypic characteristics that were atypical for strains belonging to the genus Brucella. Phenotypically many of these strains were initially misidentified as Ochrobactrum spp. Two novel species have been described so far for these strains, i.e. B. microti and B. inopinata, and other strains genetically related to B. inopinata may constitute other novel species as well. In this study we analysed the lipolysaccharides (LPS; smooth (S) and rough (R)) of these atypical strains using different methods and a panel of monoclonal antibodies (MAbs) directed against several epitopes of the Brucella O-polysaccharide (O-PS) and R-LPS. Among the most striking results, Brucella spp. strain BO2 isolated from a patient with chronic destructive pneumonia, showed a complete distinct S-LPS profile in silver stain gels that looked more similar to enterobacterial S-LPS. This strain failed also to react with MAbs against Brucella O-PS epitopes and showed weak reactivity with anti-R-LPS MAbs. B. inopinata reference strain BO1 displayed an M-dominant S-LPS type with some heterogeneity relative to the classical M-dominant Brucella S-LPS type. Australian wild rodent strains belonging also to the B. inopinata group showed a classical A dominant S-LPS but lacked the O-PS common (C) epitopes as previously reported for B. suis biovar 2 strains. Interestingly, some strains failed also to react with anti-R-LPS MAbs, like the B. microti reference strain and B. inopinata BO1 suggesting modifications in the core-lipid A moiety of these strains. These results have several implications for serological typing and serological diagnosis and underline the need of novel tools for detection and correct identification of such novel emerging Brucella spp.