The spatial organization and differentiation of the gut immune system was studied using immunohistochemistry from Embryonic Day 15 until adulthood. Leukocyte common antigen-positive cells were detected first, followed by macrophages, B, and then T lymphocytes increasing in number and intensity of staining until adulthood. The adult mouse displays regional localization of gut immune cells with highest expression in proximal intestine, decreasing distally to ileum with the fewest cells present in colon. The role of intestinal contents, bone marrow, and thymus on maturation of the gut immune system during development was studied using an isograft model: small intestine from neonatal mice were implanted subcutaneously into SCID mice and developed into morphologically normal intestine. Injected syngeneic mononuclear cells recirculated to the isografted intestine and SCID host intestine with the same regional expression as normal adult. This model is useful to define the mechanisms that establish and maintain cellular and regional differentiation of the normal gut immune system.