The tight junction (TJ) protein family of claudins is a major determinant of barrier properties in a wide variety of epithelia. Aim of the study was to compare epithelial barrier properties with the presence of TJ proteins in exactly defined intestinal segments. Transepithelial resistance (R(t)) of duodenum, jejunum, ileum and colon tissue preparations was measured in Ussing chambers. In parallel, expression of TJ proteins was analyzed by Western blots. Colon was characterized by higher R(t) than more proximal segments. However, among the small intestinal segments, R(t) was highest in duodenum and lowest in ileum. Along the intestine different claudins were detected by Western blotting with different signal intensities. Colon showed strongest signals for sealing claudins in accordance with R(t), whereas predominant expression of permeability-mediating claudins was observed in small intestinal segments. Along the intestine, claudins show a marked segment-specific expression which is in accordance with respective barrier properties.