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Cell barriers are essential for the maintenance and regulation of the microenvironments of the human body. Cell-penetrating peptides have simplified the delivery of bioactive cargoes across the plasma membrane. Here, the passage of three cell-penetrating peptides (transportan, the transportan analogue transportan 10, and penetratin) across a Caco-2 human colon cancer cell layer in vitro was investigated. The peptides were internalized into epithelial Caco-2 cells as visualized by indirect fluorescence microscopy and quantified by fluorimetry. Studies of peptide outflow from cells showed that the peptides were in equilibrium across the plasma membrane. The ability of the peptides to cross a Caco-2 cell layer was tested in a two-chambered model system. After 120 min, 7.0%, 2.8% and 0.6% of added transportan, transportan 10 and penetratin respectively was detected in the lower chamber. Both transportan and transportan 10 reversibly decreased the trans-epithelial electrical resistance of the barrier model, with minimum values after 60 min of 46% and 60% of control respectively. Penetratin did not affect the resistance of the cell layer to the same extent. Although transportan markedly increased the passage of ions, the paracellular flux of 4.4 kDa fluorescein-labelled dextran was limited. In conclusion, the results indicate that the transportan peptides pass the epithelial cell layer mainly by a mechanism involving a transcellular pathway.