The intestinal microflora can be considered as a postnatally aquired organ composed of a large diversity of bacterial cells that can perform different functions for the host. This organ is highly exposed to environmental influences and thus modulated in its composition and functions by external factors, such as nutrition. Specific components of the intestinal microflora, including lactobacilli and bifidobacteria, have been associated with beneficial effects on the host, such as promotion of gut maturation and integrity, antagonisms against pathogens and immune modulation. In addition, the microflora seem to play a significant role in the maintenance of intestinal immune homeostasis and prevention of inflammation. At the present time, the contribution of intestinal epithlial cell in the first line of defence against pathogenic bacteria and microbial antigens has been recognized, in contrast, the interactions of intestinal epithelial cells with commensal bacteria are less understood. The present work summarizes the increasing scientific attention for mechanisms of the innate immune response of the host to different components of the autochthonous microflora and suggests a potential role for selected probiotic bacteria in the regulation of intestinal inflammation.