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Peyer's patches are secondary lymphoid organs, named after the 17th-century Swiss anatomist Johann Conrad Peyer. They are aggregations of lymphoid tissue that are usually found in the lowest portion of the small intestine (ileum) in humans; as such, they differentiate the ileum from the duodenum and jejunum in that the number of Peyer's patches increase further down the intestine (ie. terminal ileum contains most Peyer's patches).

Peyer's patches are observable as elongated thickenings of the intestinal epithelium measuring a few centimeters in length. Microscopically, Peyer’s patches appear as oval or round lymphoid follicles (similar to lymph nodes) located in the lamina propria layer of the mucosa and extending into the submucosa of the ileum.

In adults, B lymphocytes are seen to predominate in the follicles' germinal centers. T lymphocytes are found in the zones between follicles.

Because the lumen of the gastrointestinal tract is exposed to the external environment, much of it is populated with potentially pathogenic microorganisms. Peyer's patches thus establish their importance in the immune surveillance of the intestinal lumen and in facilitating the generation of the immune response within the mucosa.

Pathogenic microorganisms and other antigens entering the intestinal tract encounter macrophages, dendritic cells, B-lymphocytes, and T-lymphocytes found in Peyer's patches and other gut-associated lymphoid tissue (GALT).

Peyer's patches contain specialized cells called M cells which sample antigen directly from the lumen and deliver it to antigen-presenting cells (located in a unique pocket-like structure on their basolateral side). B-cells and memory cells are stimulated upon encountering antigen in Peyer's patches. These cells then pass to the mesenteric lymph nodes where the immune response is amplified. Activated lymphocytes pass into the blood stream via the thoracic duct and travel to the gut where they carry out their final effector functions.

Although important in the immune response, excessive growth of lymphoid tissue in Peyer’s patches is pathologic, as hypertrophy of Peyer’s patches has been closely associated with idiopathic intussusception.

The hypertrophy of Peyer's patches has also been associated with susceptibility to transmissible spongiform encephalopathies (commonly known as prion diseases).