Members of the claudin protein family are key regulators of tight junction selectivity and are implicated in influencing development and cellular differentiation in the intestine and other tissues. The goal of the present study was to profile claudin gene expression and protein location during postnatal development of the mouse jejunum and in the adult mouse gut from duodenum to distal colon as a first step in understanding both normal claudin function and the pathologic implications of altered expression patterns. The relative expression of claudins 1-19 and other tight and adherens junction genes was determined by quantitative RT-PCR from six regions of normal mouse intestine and colon. Immunofluorescent localization was performed for claudins 1-5, 7, 8, 10, 12, 15, and 18. Transcripts for claudins 1-5, 7-13, 17, and 18 were all detected in adult intestine, although their relative abundance differed up to 1000-fold within individual segments. In contrast to the unchanging expression and localization of ZO-1, occludin, and JAM, most claudins were expressed in decreasing or increasing gradients or in more complex patterns along the longitudinal axis of the intestine and the crypt to villus/surface differentiation axis. During neonatal development at days 1, 14, 28, and 90 several claudins showed striking increases or decreases in transcript expression as well as changes in tissue localization along the crypt-villus axis. Claudin-19 was only detected at days 1 and 14. This database provides a resource for investigating regional and developmental differences in permselectivity, crypt to villus/surface differentiation and neoplastic changes along the gut and during postnatal development.