The mammalian intestine harbours one of the most dense microbial communities on the planet. Experiments that compare germ-free and colonised mice show that the mucosal immune system is highly adapted to the presence of the commensal microbiota. To induce mucosal immune responses to commensal intestinal bacteria, small numbers of commensals are sampled by dendritic cells (DC) at the epithelial surface. These locally induce IgA B cells through T-dependent and T-independent pathways, but they do not penetrate beyond the mesenteric lymph nodes to reach systemic secondary lymphoid structures. Experiments where colonisation of the intestine has been uncoupled from mucosal immune induction with live commensals show that the resulting response is very long-lived unless another response is induced by stimulation with a different commensal microbe. Adaptive immunity in pathogen-free experimental mice is normally ignorant of intestinal commensals. Nevertheless, there is a threshold set by innate immunity, which can strengthen the epithelial barrier and allow clearance of small numbers of commensals that escape the permeability barrier or are released by ,commensal loaded’ DC. Defective innate clearance is compensated functionally by increased systemic adaptive responses to intestinal commensals, showing a continuum between innate and adaptive immunity.