Mucosal lymphocyte homeostasis involves the dynamic interaction of enteric microbiota, the intestinal host epithelium, and the mucosal immune system. Dysregulation of mucosal lymphocyte homeostasis results in a variety of intestinal disorders, notably inflammatory bowel diseases like ulcerative colitis and Crohn's disease. One key cellular component regulating homeostasis are B lymphocytes that reside in gut-associated lymphoid tissue. This compartment includes Peyer's patches, isolated lymphoid follicles, lamina propria, and mesenteric lymph nodes. Recent data have pointed to two new and exciting aspects of B cells in the gut. First, there has been progress on identification and functional analysis of abundant isolated lymphoid follicle B cells that are key mediators of IgA genesis. Second, several groups have now clarified the functional identification and characterization of immunoregulatory B cells in the gut. This review examines the novel aspects of these B cells, and examines how each plays a role in mediating mucosal homeostasis in this bacteria-laden compartment.