Probiotics are viable microorganisms which after consumption, dependently on the strain and dose, exert beneficial effect on the host's organism. Lactic acid bacteria Lactobacillus and Bifidobacterium and selected strains of Streptococcus, Bacillus as well as Saccharomyces boulardii yeast are most frequently used as probiotics. Probiotics have a favourable effect on the composition of alimentary tract ecological environment demonstrating antagonism in relation to numerous pathogenic microorganisms colonizing gastrointestinal mucosa. The presence of fermentative bacteria in the intestine, mainly lactic acid bacilli, particularly adhesive types prevents from bacterial dislocation and enterotoxemia, normalizes intestinal motor activity disorders and diminishes the symptoms of lactose intolerance. Prebiotics are substances naturally contained in food (or added to it) which selectively stimulate growth and/or activity of some strains of probiotic bacteria found in the alimentary tract. Probiotics and prebiotics as well as their combination - synbiotics are found in food, milk mixtures, pharmacological preparations, food additives, dietary supplements and they improve in a natural way our health condition and are of greater importance 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 diseases in children, such as: bacterial and viral diarrhoea, antibiotic-induced disbiosis, necrotizing enterocolitis, intestinal colic, non-specific enteritis, alimentary tract dysfunction.