The spontaneous formation of amorphous drug nanoparticles following the release of a drug from a supersaturating formulation is gaining increasing attention due to their potential contribution to increased oral bioavailability. The formation of nanosized drug particles also has considerable implications for the interpretation of in vitro and in vivo data. However, the membrane transport properties of these drug particles remain less well understood. Herein, the membrane permeation of nanosized amorphous drug particles of a model drug atazanavir was evaluated using different artificial membrane-based, cell-based, and animal tissue-based models. Results showed that flux enhancement by particles was different for the various systems used. Generally, good agreement was obtained among experiments performed using the same apparatus with different model membranes, with the exception of the Madin-Darby canine kidney cell monolayer and the Long-Evans rat intestine tissue, which showed lower flux enhancements. Franz cell-based models showed slightly higher flux enhancements by particles compared to Transwell and intestinal tissue sac models. Mass transport analysis suggested that the extent of flux enhancement by particles is dependent on the geometry of the apparatus as well as the properties of the membrane and buffer used, whereas the flux plateau concentration is dependent on the unstirred water later (UWL) asymmetry. These results highlight the complexity in characterizing the permeability advantage of these nonmembrane permeable drug particles and suggest that caution should be used in selecting the appropriate in vitro model to evaluate the overall permeability of colloidal drug particles.