Gut-associated lymphoreticular tissues, such as Peyer's patches and cecal patches, are important inductive sites for mucosal immune responses. As such, gut-associated lymphoreticular tissues may have an epithelial barrier different from that of villous epithelium. In this study, we investigated the immunohistochemical distribution of the claudin family and occludin in the follicle-associated epithelium (FAE) of Peyer's patches and cecal patches of murine intestine. Unique profiles of claudin-2, -3, and -4 and occludin expression were noted in the tight junctions of the FAE: claudin-4 was preferentially expressed in the apex region; claudin-2 was only weakly expressed on the crypt side of the FAE compared with stronger expression on the crypt side of villous epithelial cells; and claudin-3 and occludin were found throughout the dome. These unique expression patterns were present also in cecal patch FAE. We also found that claudin-4 expression in the FAE of Peyer's patches and cecal patches correlated with the presence of TUNEL (terminal deoxynucleotidyl transferase-mediated dUTP nick-end labeling)-positive apoptotic cells, and Peyer's patch-deficient mice exhibited expression patterns of claudin and occludin in villous epithelia similar to those in wild-type mice. We conclude that claudin-4 expression was preferentially associated with the dome region of FAE, the mucosal inductive site of the murine intestine. In that location it might correlate with the cell life cycle, help maintain the apex configuration of the dome, or be a factor favoring the uptake of antigens by the FAE.