Lymphoid organogenesis is dependent upon a series of intricate cellular interactions involving adhesion molecules, chemokines, and cytokines that generate fully compartmentalized lymphoid structures. Development of organized lymphoid structures in the intestine begins prenatally and continues through adulthood, with constant adaptations to changes in the luminal flora. While much is known about the mechanisms that govern the development of macroscopic intestinal lymphoid structures (mesenteric lymph node and Peyer's patches), the organogenesis of the microscopic lymphoid tissues (including cryptopatches and isolated lymphoid follicles) is an emerging field. This review examines the current state of knowledge about organogenesis of the known types of organized lymphoid tissue in the intestine and identifies unique and common features in the development of each of the structures discussed.