Human colon is harboured by a complex ecosystem containing up to 1000 species of microorganisms. The intestinal microbiota play a crucial role in the metabolism of food components and in ensuring health. Many products of the metabolism can favour the development of colon tumours. The main role in the formation of carcinogenic compounds play bacterial enzymes such as: β glucuronidase, β-glucosidase, nitroreductase, 7-α-dehydroxylase, β-galactosidase, and azoreductase. Their products can be compounds harmful to human health, such as: phenolic and indolic compounds, flavonoid aglycones, azo dyes, fecapentaens, oestrogens, and secondary bile acids.