Purpose. The interaction of nanoparticles (NP), consisting of hydrophobic polystyrene, bioadhesive chitosan, and stealth PLA-PEG with two human intestinal cell lines, the enterocyte-like Caco-2 and mucus-secreting MTX-E12, was investigated and compared to the in vivo NP uptake in rats. Methods. The extent and mechanism of cellular association of different NP with Caco-2 and MTX-E12 was investigated using confocal laser scanning microscopy (CLSM) and a cellular association assay. In vitro results were compared to gastrointestinal distribution of chitosan NP in rats after intra-duodenal injection. Results. Cellular association of NP with Caco-2 cell monolayers showed the following rank order: polystyrene > chitosan >> PLA-PEG. Mucus (MTX-E12) significantly decreased the association of hydrophobic polystyrene NP. While no mucus binding was observed for PLA-PEG, association of chitosan NP with mucus strongly increased. Intra-duodenal administration of chitosan NP in rats confirmed these in vitro results, demonstrating that NP could be detected in both epithelial cells and Peyer's patches. Chitosan NP internalization was saturable, as well as energy- and temperature-dependent. It could be inhibited by an excess of protamine and by removal of anionic sites of the apical membrane. By contrast, polystyrene NP uptake was found to be largely independent of these factors, except for a temperature-dependency. Conclusions. In contrast to Caco-2 cells, the presence of mucus presented a major barrier for the uptake of hydrophobic polystyrene NP and showed an even more profound effect upon the uptake of chitosan NP. A correlation between the uptake in cell culture models and in vivo rat epithelial cells was confirmed for chitosan NP. Moreover, chitosan NP seemed to be taken up and transported by adsorptive transcytosis, while polystyrene NP uptake was probably mediated by non-adsorptive transcytosis.