Immune cells such as macrophages and dendritic cells can be found throughout the gut lumen and are responsible for monitoring the high microbial load of the gastrointestinal (GI) system.

Gut-associated lymphoid tissues (GALTs) are local clumps of organized secondary lymphatic tissue that can serve almost as an outpost for immune cells in the GI tract.

In the small intestine only, Peyer's patches can be found which are specialized areas in the intestinal wall that comprise important local sites of immune response initiation. The patches are home to large populations of B cells as well as germinal centers to allow differentiation into plasma and memory B cells.