Objective: In addition to non-digested nutrients, human stools contain endogenous substrates, among which bacteria are a major component, whose growth may be stimulated when more dietary nutrients are available for bacterial fermentation, as in patients with malabsorption syndrome. We assessed the energy content and composition of both stools and faecal bacteria in healthy volunteers and patients with a short bowel and colon in continuity (SBC). Our goal was to clarify the magnitude of error introduced by the faecal bacteria in the measurement of the digestibility of ingested energy and nutrients. Subjects and methods: We studied six healthy volunteers and six patients with a SBC under free oral intake. The bacterial mass of stools was isolated. In the bacterial fractions and fresh stools, calorie, fat, nitrogen and short-chain fatty acid contents were determined. The Wilcoxon signed rank or the Mann-Whitney tests were used for comparison. Results: In healthy volunteers and patients with SBC, faecal bacterial mass accounted for 44 and 35% of faecal dry weight, and contained 50 and 34% of total faecal energy. In healthy volunteers, the apparent digestibilities when corrected by bacterial constituents (88-97% according to nutrients) were significantly higher than the apparent non-corrected digestibilities (84-94%). In patients with SBC, the corrected apparent digestibilities (69-89% according to nutrients) were significantly higher than the apparent non-corrected digestibilities (54-83%). Conclusion: The error introduced by the faecal bacterial fraction when assessing the extent of nutrient digestibility is small in healthy volunteers; it is more pronounced in patients with SBC, reaching 18% for the digestibility of ingested fat.