Inflammatory bowel diseases are chronic disorders. In the recent years research on this problem has intensified because of increasing incidence of IBD. The aim of the study was to compare numbers of bacteria in colon samples of children suffering from IBD and controls. The samples taken were: 2 biopsies collected during colonoscopy from both macroscopically normal or inflamed mucosa (normal one only in the control group) and stool. Tissue samples and stool were examined using a quantitative culture technique, a quantitative fluorescent in situ hybridization (FISH) method and denaturing gradient gel electrophoresis (DGGE). Moreover, thickness of intestine mucus layer and mucin degradation by bacterial gut flora were checked. The number of Bifidobacterium spp. was lower in all examined stool samples of children with IBD and also lower in tissue samples collected from the macroscopically inflamed mucosa as compared to controls. In case of tissue samples obtained from children with CD, the number of Streptococcus spp. was higher and in children with UC, the level of Lactobacillus spp. increased, as compared to control tissue samples. Described changes in the composition of the bacterial flora in the colon were of a qualitative character. Faecal flora in patients with IBD was richer in aerobic bacteria than in the control group. Moreover, the inflammatory process taking place in the intestines of children with IBD caused a thinning of the mucus layer lining the intestinal wall and the faecal flora in patients with UC the had ability do digest mucin in vitro.