The conditions occurring in the large intestine, including benign environment, regular supply of substrates, regular emptying, and long transit time, create the most friendly habitat for microbial growth found within the whole gastrointestinal tract. The normal adult colon contains ~200 g of digesta, of which ~60% (dry weight basis) are microorganisms. Colonic microflora comprises ~10 dominating genera reaching the mean population numbers of 10⁸-10¹⁰ cells per gram of contents. However, they were determined in a wide range of several log cycles in individuals, significantly influenced by host diet providing colonic food as substrates for bacterial growth and development. The activity of microflora makes large intestine the organ with the greatest metabolic activity in the whole body. Close contact of a variety and multiplicity of microbes as well as microbes and host, via enterocytes and gut-associated lymphoid tissue, produces interaction with epithelium resulting in systemic effects. Therefore, it seems reasonable to address the colon as target-place of probiotics and prebiotics exerting microflora-mediated effects. Their implementation to more and more western-type diet may result in the improvement of the health status of the population. Moreover, they also seem to be promising in clinical cases, however that statement needs confirmation in the controlled clinical trials. The review passes around scientific knowledge on the microecosystem of colon being the basis for use of probiotics and prebiotics as functional food compounds.