It is probably one of the most complex tasks to understand the mutual relationship between members of the microbial community in the gut and their interaction with the host. Although many animals including humans can live without gut flora, it is beneficial for the growth and protection of the host against pathogens. On the other hand, clinical and experimental intestinal inflammatory reactions have been attributed to immune recognition of the intestinal microflora. This review discusses recent and old findings on function and immunological relevance of the endogenous microflora.