The intestinal lymphoid follicles and associated structures are specialised antigen sampling and inductive sites of the mucosal immune system. The overlying follicle-associated epithelium (FAE) includes the specialised antigen sampling M cells that are also exploited as a route of pathogen invasion. In this immunohistochemical study we analysed the junctional complexes of the mouse intestinal FAE. Protein expression at this site resembled that of other simple epithelia. Specifically, claudin-1/3 and ZO-1 were detected in the tight junctions, E-cadherin, alpha-, beta- and gamma-catenin, vinculin, alpha-actinin and polymerised actin were associated with the adherens junctions and the desmosomes were labelled with a desmosomal protein probe. These markers failed to reveal cell type-associated variations in the tight junctions and desmosomes. In contrast, M cell adherens junctions were distinguished by enhanced expression of beta-catenin, alpha-actinin, polymerised actin and, in some areas, E-cadherin. In addition, M cell junctions exhibited increased expression of intercellular adhesion molecule-1 and phosphotyrosine, and the M cell apical surfaces displayed characteristic patterns of beta-catenin, alpha-actinin and actin expression. We have thus partially defined the junctional complexes of mouse intestinal FAE and identified M cell-specific characteristics that may further explain the biology and function of this unique cell type.