Pathogenic mycobacteria, including those that cause tuberculosis and paratuberculosis, cross mucosal barriers by endocytosis within mucosal lymphoepithelial sites. These entry sites commonly include oropharyngeal and nasopharyngeal tonsils and Peyer's patches. Bacilli discharged at the basolateral surfaces of engulfing epithelial M cells are taken up by professional antigen-presenting cells associated with T lymphocytes of the parafollicular area. Dendritic cells and macrophages in these sites allow mycobacterial replication, due to the permissive immunological environment in lymphoepithelial tissues. Abrogation of local delayed-type hypersensitivity reactions generally ensures continuing integrity and function of these tissues. Phagocytes containing intracellular mycobacteria disseminate infection to other parts of the body and also probably migrate back onto the mucosal surface to shed bacilli.