Colonization with bacteria is critical for the normal structural and functional development and optimal function of the mucosal immune system. Unrestrained mucosal immune activation in response to bacterial signals from the lumen is, however, a risk factor for inflammatory bowel disease. Therefore, mucosal immune responses to indigenous flora require precise control and an immunosensory capacity for distinguishing commensals from pathogens. The use of germ-free animal models with selective colonization strategies combined with modern molecular techniques promises to clarify the molecular signals responsible for host-flora interactions in health and disease. At least half of the resident flora cannot be cultured by conventional techniques but are identifiable by molecular methods. Collectively, the resident flora represent a virtual organ with a metabolic activity in excess of the liver and a microbiome in excess of the human genome. An improved understanding of this hidden organ holds secrets relevant to several infectious, inflammatory and neoplastic disease mechanisms.