Indigenous microorganisms of many genera and species associate with mucosal epithelia in the gastrointestinal tracts of animals and humans. These mechanisms may involve a high degree of specificity for host and surface habitat. They may include a capacity of the microorganisms to adhere to the membranes of substratum epithelial cells, to colonize and utilize as a source of nutrients the mucus overlying epithelial cells, and to be motile and attracted into the mucous layer by chemotaxis. The microbes must be able as well to thrive in the nutritional and environmental conditions prevailing on the epithelial surfaces. Microbial communities associated with epithelial surfaces are critical for maintaining a microflora in areas of the tract (i.e., stomach, small intestine) where the lumenal content moves at a rate exceeding the maximum rates at which indigenous microorganisms can multiply. Such communities even may be important in areas (i.e., the cecum and colon) where the content moves at rates below those at which the microbes can multiply. In such areas, microorganisms colonizing mucus on the epithelium and in the crypts of Lieberkuhn may provide a stable inoculum for the lumenal content which may be altered in composition in times of dietary change. Microorganisms associated with gastric and intestinal surfaces undoubtedly serve in a major way to stabilize the composition of the indigenous gastrointestinal microflora. At the molecular level, however, little is known about the mechanisms stabilizing the composition or the biochemical and genetic activities of the microflora. Such mechanisms are important subjects for research in the future.