Probiotics are viable microorganisms which being consumed in a proper dose exert beneficial effects on the host. Lactic acid bacteria Lactobacillus and Bifidobacterium and selected strains of Streptococcus, Bacillus, yeast Saccharomyces boulardii are most frequently used as probiotics. Dependently on the strain and the dose probiotic bacteria restore natural properly functioning system of intestinal flora, inhibit the development of numerous pathogenic microorganisms, alleviate the course and shorten the duration of bacterial and viral diarrhoea, prevent the occurrence or relieve antibiotic-associated diarrhoea, eliminate or diminish the symptoms of lactose intolerance as well as normalize intestinal motor activity disorders. Prebiotics are substances contained in food (or added to it) which selectively stimulate the growth and/or activity of some strains of probiotic bacteria found in the alimentary tract. Prebiotics improve the content of intestinal biocenosis, intestinal motor activity, regression of clinical symptoms of intestinal inflammatory diseases and have a beneficial effect on intestinal epithelial cells nourishment by stimulation and creation of conditions for the growth of probiotic strains. Probiotics, prebiotics as well as their combination – synbiotics improve in a natural way by multidirectional therapeutic effect of viable bacterial cultures, our health condition, contribute to pharmacological therapy and are more and more important in modern medicine. The study presents the share of probiotics and prebiotics in the formation of alimentary tract biocenosis and their application in the prophylaxis and treatment of selected gastrointestinal diseases.