Understanding the dynamics of the establishment of C. difficile within the gut is vital to effective prevention, control and therapy of disease due to this nosocomial pathogen. Factors affecting the establishment of C. difficile in the gut were investigated including the role of bacterial metabolic products (BMPs), the composition of colonic flora, diet, and properties of the infecting strain. Concentrations of 9/12 bacterial metabolic products (BMPs), both volatile and non-volatile were significantly higher in mice which eliminated oral challenge with 108 spores of C. difficile (E mice) than in mice harbouring the organism (H mice). Growth of C. difficile in vitro was inhibited 104 fold at combinations of BMPs at concentrations found in stools of E mice but not in stools of H mice. The in situ production and concentrations of BMPs were increased by augmenting the amount of fermentable fibre in the diet. This resulted in elimination of C. difficile from 6/7 C. difficile colonized mice within 6 days of beginning a diet containing 20% fermentable fibre, whereas mice fed diets containing 2% fermentable fibre or 20% non-fermentable fibre continued excreting the organism. Elimination of C. difficile was associated with increased concentrations of BMPs and changes in the numbers of organisms already present within the colonic flora. Properties of two microbial phenotypes (smooth (S), and rough (R)) of one strain of C. difficile were examined in vitro and the ID(50s) determined. The S phenotype survived, germinated and grew in media containing higher concentrations of BMPs, acquired iron when grown under iron restriction, utilized haem and bound Congo red more readily than the R phenotype. In mice fed the 2% fermentable fibre diet the ID50 for the S phenotype was 103 spores and 108 spores for the R phenotype, whereas for mice fed the 20% ferment able fibre diet it was >106 spores for the S phenotype. The ability of this opportunistic pathogen to adapt to changing environmental conditions is an important factor in determining whether the organism will colonize and cause disease. Diets supplemented with fermentable fibre may be a valuable method of preventing and treating C. difficile related disease.