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Abstract Micro- and nanoplastics (MNP) can be found virtually everywhere around us in the biosphere and food chain, therefore humans are continuously exposed to MNP, mainly via inhalation and ingestion. Here, we have applied physiologically relevant human-based advanced in vitro models representing the lung (MucilAir™) and gut (InTESTine™ and Intestinal Explant Barrier Chip (IEBC)) to study membrane passage of various MNP and their potency to induce cytotoxic effects, barrier disturbances or pro-inflammatory cell activation. Selected MNP of various materials (polystyrene, polyethylene, nylon, car tire, and marine MNP collected from the ocean), shapes (spheres, fragments and fibers), sizes (0.05–100 μm), some of which were fluorescently labelled for tracking, were included. Without affecting cell viability, nylon fibers and (cleaned) HDPE (high density polyethylene) disrupted the MucilAir™ epithelial barrier. Luminal exposure to polystyrene particles (1 and 10 μm) and pristine HDPE fragments significantly decreased human colon tissue functionality. Furthermore, all polystyrene particles (0.05, 1 and 10 μm) affected tissue viability in porcine jejunum, ileum and colon tissue after 5 h exposure, and this was further confirmed in the IEBC after 24 h of exposure to 10 μm polystyrene particles and nylon fibers. Exposure to nylon fibers and its supernatant led to pro-inflammatory cell activation, as shown by increased IL-6 release in MucilAir™ and in human colon tissue after 96 or 24 h, respectively. Regarding transepithelial penetration of the MNP, permeability of 0.05 μm polystyrene spheres in the MucilAir™ lung cell model reached 3.6 ± 1.2% after 24 h. With 3.37 ± 0.46% after 5 h under static conditions and 5.5 ± 1.3% after 24 h under microfluidic conditions MNP permeability across intestinal tissue was highest for the largest (10 μm) polystyrene spheres. Confocal microscopy confirmed the translocation of MNP across the lung and intestinal epithelial barrier. In conclusion, we present a study revealing the passage of MNP over the epithelium of advanced in vitro models for the lung and intestine barrier. Furthermore, pro-inflammatory cell activation and disrupted barrier integrity were observed after exposure to several of the tested MNP. Future research is needed to further identify the effects of shape, size and material on these processes and subsequently the health effects of humans.