Approximately 70% of the immune system is localized in the gastrointestinal tract. The saliva and gastrointestinal secretions, as well as flora (probiotics) and supplied fibres (prebiotics), are important for optimal function. Probiotic bacteria have been shown to influence the immune system through several molecular mechanisms. Pre-, pro- and synbiotics (products produced by fermentation) offer both protection against and cure of a variety of endemic and acute diseases. This review summarizes the present experience in various forms of diarrhoea, inflammatory bowel disease, and Helicobacter infections, in intensive care patients and in connection with extensive surgery.