Colonic mucins of germ-free (GF) and conventional rats (CV) were compared. After isolation by gel filtration on Sepharose CL-4B and purification by density gradient centrifugation, the content of isolated colonic mucins was estimated by determination of PAS positive carbohydrates. Purified mucins were subjected to carbohydrate and amino acid analysis and separated into mucin subclasses by ion exchange chromatography. While the total amount of colonic mucins was not statistically different in GF and CV animals, analysis of carbohydrate composition demonstrated an increased amount of sialic acid in CV rat mucin. This was in accordance with results of ion exchange chromatography, revealing a significant higher amount of negative charged mucin subclasses in CV mucin, compared to the germ-free counterpart. The results of amino acid analysis were similar in both groups. The compositional differences in carbohydrate moieties are attributed to modulations by the intestinal flora. A selective bacterial degradation of the neutral mucin subclasses and modifications in the mucin composition due to a stimulated synthesis are discussed.