The influence of inulins with different average degree of polymerization (ranging from 3 to 25) on the metabolic activity of the human colonic microbiota with or without the addition of Clostridium difficile was investigated in vitro. The in vitro system used was a dynamic, computer-controlled model that simulates the conditions of the proximal part of the large intestine with peristaltic mixing, water absorption and absorption of fermentation products. The addition of inulin stimulated the formation of the total amount of short-chain fatty acids acetate, propionate and butyrate up to 50%, and lactate > 10-fold for short-chain inulin, while the formation of ammonia and the branched-chain fatty acids iso-butyrate and iso-valerate was suppressed. Ammonia formation was suppressed by about 30% and that of iso-butyrate and iso-valerate was almost completely suppressed. These effects became much more pronounced when C. difficile was present in the system. The introduction of C. difficile caused a stimulation of the production of the protein fermentative metabolites ammonia, branched-chain fatty acids and the phenolic compounds indole, phenol and p-cresol. This stimulatory effect of C. difficile was almost completely prevented by the addition of inulins. Thus, these results indicate a potential of inulins to shift the metabolic activity of the human colonic microbiota towards the production of less potentially toxic metabolites, both under normal conditions and under conditions with a disturbed microbiota (with a high level of C. difficile).