Transfer of the shuttle vector pRRI207 mediated by the helper plasmid pRK2013 from Escherichia coli to Bacteroides spp. was possible in vitro and in vivo in the digestive tract of axenic mice associated with Bacteroides uniformis 1004 or Bacteroides vulgatus of human origin. In vivo, transfer frequencies were nearly identical for B. uniformis (2×10−7) and B. vulgatus (4×10−7) and the transconjugant strains of B. uniformis and B. vulgatus became established in the digestive tract of mice at densities ranging from 102–103 to 104 CFU g−1 of faeces, respectively. Transfer from E. coli to Bacteroides strains in gnotoxenic mice associated with human faecal flora (HFF) was not successful. Transconjugant-like clones appeared among the HFF of gnotoxenic mice after they were inoculated with B. uniformis TBUA, a transconjugant strain of B. uniformis 1004 obtained from triparental mating and which harboured the shuttle vector. Hybridisation showed that the shuttle vector pRRI207 was not present in these clones, and it is suggested that they could result from the transfer of a conjugative transposon ERL contained in B. uniformis 1004. Moreover, clones believed to have lost the shuttle vector hybridised with a specific probe to B. thetaiotaomicron and therefore did not originate from B. uniformis TBUA.