Studies with immunodeficient and knockout mice have revealed that the development of mucosa-associated lymphoid tissues (MALT) and peripheral lymphoid nodes share common mechanisms, but also require distinct signals. Gene disruption of lymphotoxins or their cognate receptors affects both Peyer's patch and lymph node organogenesis. Disruption of the osteoprotegerin TNF-family member gene does not impair Peyer's patch development, but prevents formation of peripheral lymph nodes. Peyer's patch do not form in mice with a deleted gene encoding a B lymphocyte-specific chemokine receptor, while most peripheral lymph nodes, except inguinal, are normal in numbers and architecture. In B or T lymphocyte-deficient mice, Peyer's patches, with their overlying follicle-associated epithelium (FAE), are present although reduced in number and size. No Peyer's patches develop in RAG deficient mice. Formation of FAE with typical M cells has not been analyzed in these mice. M cell formation requires the close association of immune cells with differentiated enterocytes and their conversion appears to be transcriptionally regulated. The development of MALT, FAE and probably M cells is a multistep process that requires signalling pathways common to all secondary lymphoid tissues, but also MALT-specific factors.