Commensal organisms associated with areas of the host exposed to the external environment are collectively termed the microbiota. Whilst poorly understood environmental and genetic factors influence the development of the large intestinal microbiota, the relative contributions of host genetics vs. the environment remain unknown. Faeces was selected as a paradigm for gut microflora comparison studies since 16S rRNA PCR-DGGE derived fingerprints from intestinal lumen, mucosa and faeces were highly similar. DGGE analysis of faeces from five highly inbred strains of mice housed and bred at Manchester University (C3H, C57. GFEG, CBA and CD1), showed that mice of the same strain harboured highly similar fingerprint profiles that were characteristic for each individual mouse strain.