Epithelial barriers on mucosal surfaces at different sites in the body differ dramatically in their cellular organization, and antigen sampling strategies at diverse mucosal sites are adapted accordingly. In stratified and pseudostratified epithelia, dendritic cells migrate to the outer limit of the epithelium, where they sample antigens for subsequent presentation in local or distant organized lymphoid tissues. In simple epithelia, specialized epithelial M cells (a phenotype that occurs only in the epithelium over organized lymphoid follicles) deliver samples of foreign material by transepithelial transport from the lumen to organized lymphoid tissues within the mucosa. Certain pathogens exploit the M cell transport process to cross the epithelial barrier and invade the mucosa. Here we review the features of M cells that determine antigen and pathogen adherence and transport into mucosal lymphoid tissues.