When considering the inhalation of high-aspect ratio nanoparticles (HARN), the characterization of their specific interaction with lung cells is of fundamental importance to help categorize their potential hazard. The aim of the present study was to assess the interaction of cellulose nanocrystals (CNCs) with a multicellular in vitro model of the epithelial airway barrier following realistic aerosol exposure. Rhodamine-labeled CNCs isolated from cotton (c-CNCs, 237 ± 118 × 29 ± 13 nm) and tunicate (t-CNCs, 2244 ± 1687 × 30 ± 8 nm) were found to display different uptake behaviors due to their length, although also dependent upon the applied concentration, when visualized by laser scanning microscopy. Interestingly, the longer t-CNCs were found to exhibit a lower clearance by the lung cell model compared to the shorter c-CNCs. This difference can be attributed to stronger fiber-fiber interactions between the t-CNCs. In conclusion, nanofiber length and concentration has a significant influence on their interaction with lung cells in vitro.