In mice, commensal bacteria are shown to provide critical signals that limit bacterial trafficking to the mesenteric lymph nodes by immune cells, thus preventing the induction of mucosal immune responses. A critical question in the field of intestinal immunology is how the immune system can mount protective immune responses against pathogens while avoiding such responses against useful or commensal organisms. Gretchen Diehl et al. show that commensal bacteria provide critical signals that limit the trafficking of CX3CR1hi phagocytic or dendritic lamina propria cells to the mesenteric lymph nodes, thus inhibiting the induction of mucosal immune responses. Therapeutic modulation of these cells may attenuate intestinal inflammation or enhance priming for mucosal vaccines. The intestinal microbiota has a critical role in immune system and metabolic homeostasis, but it must be tolerated by the host to avoid inflammatory responses that can damage the epithelial barrier separating the host from the luminal contents1,2,3,4,5,6. Breakdown of this regulation and the resulting inappropriate immune response to commensals are thought to lead to the development of inflammatory bowel diseases such as Crohn’s disease and ulcerative colitis7. We proposed that the intestinal immune system is instructed by the microbiota to limit responses to luminal antigens. Here we demonstrate in mice that, at steady state, the microbiota inhibits the transport of both commensal and pathogenic bacteria from the lumen to a key immune inductive site, the mesenteric lymph nodes (MLNs). However, in the absence of Myd88 or under conditions of antibiotic-induced dysbiosis, non-invasive bacteria were trafficked to the MLNs in a CCR7-dependent manner, and induced both T-cell responses and IgA production. Trafficking was carried out by CX3CR1hi mononuclear phagocytes, an intestinal-cell population previously reported to be non-migratory8. These findings define a central role for commensals in regulating the migration to the MLNs of CX3CR1hi mononuclear phagocytes endowed with the ability to capture luminal bacteria, thereby compartmentalizing the intestinal immune response to avoid inflammation.