The intestine contains the greatest number and diversity of immune compartments in the body. These compartments can be broadly classified into intestinal inductive and effector sites: Intestinal inductive sites represent the sites in which adaptive immune cells undergo initial priming and differentiation in the intestine and comprise the intestinal draining mesenteric lymph nodes and the gut associated lymphoid tissues (GALT), the latter including the macroscopically visible Peyer’s patches of the ileum and the much more numerous isolated lymphoid follicles that are distributed along the entire length of the intestine. Intestinal effector sites include the intestinal lamina propria and epithelium in which primed adaptive immune cells localize and are maintained to promote barrier integrity and protective immunity. Here I will discuss some of our latest and unpublished work aimed at dissecting immune composition and function in these distinct niches of the human intestine in health and disease.