The immune system is organized as a number of distinct lymphoid organs interconnected by recirculating lymphocytes. These organs, such as lymph nodes, spleen, and gut-associated Peyer's patches, are compartmentalized, providing separate niches for T and B cells. In addition, regional compartmentalization of lymphoid organs themselves exists, leading to the distinction between the mucosal and the systemic immune systems. This distinction not only reflects the anatomical localization but also is based on functional differences, with predominant tolerance induction via mucosal routes and immunity seen after systemic antigen exposure. These differences are associated with regional differences in the lymphoid organs and with environmental conditions of the tissues in which the immune system functions. Recirculation patterns of lymphocytes differ between mucosal and systemic lymphoid organs, and more insight into the mechanisms that imprint this behavior has been generated recently. Differences in dendritic cells have been observed between mucosal and systemic sites, and knowledge on how local factors contribute to the immune system is emerging. From our studies on mucosal tolerance in mouse models, it has become evident that regional lymph nodes draining the mucosa are important sites to direct immune responses. Here, we discuss the way regional lymph nodes contribute to the direction of immune responses and what is known about the local factors and cell behavior that form the basis for these differences.