Lyme arthritis is caused in Europe by three main pathogenic species of Borrelia burgdorferi sensu lato: Borrelia burgdorferi sensu stricto, Borrelia garinii, and Borrelia afzelii. Because few synovial samples have yet been analysed by species-specific DNA amplification methods, further studies are needed to define the spectra of clinical manifestations associated with these different species. Two cases of treatment resistant Lyme arthritis are reported here, in which DNA amplification of the flagellin gene followed by dot-blot hybridisation in the synovial fluid identified B garinii as the causative agent. Clinical and biological data did not differ from the usual descriptions of Lyme arthritis, but as the recently reported molecular mimicry between OspA and hLFA1 is not applicable to B garinii, the pathogenesis of the present cases remains unclear. Future studies should aim at assessing the role of B garinii in European Lyme arthritis and its possible pathogenic and therapeutic consequences.