Forty eight male Wistar rats were divided into 6 groups and fed over 4 weeks with diets containing 2.5, 5 or 10% addition of potentially inert carbohydrate cellulose (CEL) or easily fermentable fructooligosaccharides (FOS). In rats fed on CEL diets no substantial changes in the pH, caecal mass, as well as protein, ammonia and short-chain fatty acids (SCFA) concentration in the caecal digesta were observed; almost all microbial enzymes activity also was not modified, except the activity of β-glucuronidase which decreased considerably upon higher doses of CEL (5 and 10%). Lower FOS supplementation (2.5 and 5%) led to desirable changes typical for dietary fructans (increased SCFA concentration and acidification of digesta), while the 10% addition of FOS had some unfavourable effects such as decreased SCFA concentration, especially butyrate, and excessive enlargement of the caecum (tissue and digesta). In conclusion, 10% addition of FOS seems to be an overdose, while CEL can be recognized as a good negative control in experiments with non-digestible saccharides, however, its influence on microflora activity should be considered during the interpretation of the obtained results.