The intestinal tract performs many different functions; in addition to absorption and digestion it is also the body's largest organ of host defence. Part of the intestinal mucosal barrier function is formed by a common mucosal immune system which provides communication between the different mucosal surfaces of the body. The intestine also contains a microbial ecosystem with a large body of microbes, 1-11/2 kg in an adult. The microbes and their activity have a major impact on the development and functioning of the intestinal immune system and vice versa. This mutual influence also affects the host beyond the intestine. The intestinal colonisation with a balanced microflora is of main importance for the correct development of the immune system. The importance of the intestinal microflora is most clearly seen in germfree animals, but also diseases like atopy are associated with disturbances in the intestinal microflora. This often manifests itself in a low number of bifidobacteria. The use of probiotics or prebiotics to correct this imbalance and modulate the immune activity has received increasing scientific documentation. The precise mechanisms behind these immune modulatory activities are not well understood and require further investigation.