Here, we assessed a co-culture system of intestinal Caco-2 cells and lymphoblastoid TK6 cells for modelling the role of intestinal first-pass effects, i.e. absorption and metabolism, in the genotoxicity of oral drugs and food contaminants. Caco-2 cells were seeded onto semipermeable culture inserts for 21 days until differentiation, and then TK6 cells were added to the basal compartment. After apical loading with mutagenic compounds [methylmethanesulfonate (MMS), benzo[a]-pyrene (BaP) and aflatoxin B1 (AFB1)], comet and micronucleus assays were performed on both cell lines. MMS (10 µg/ml) showed positive results in the micronucleus assays in both cell lines, even though DNA damage was only detected in the Caco-2 cells with the comet assay. At concentrations of 0.5-50 µM, BaP induced dose-dependent comet and micronucleus formation at 24h in Caco-2 cells, but no DNA damage was observed in TK6 cells. Although AFB1 failed to induce comet formation, it resulted in a high level of micronuclei in both cell lines. Treatment of Caco-2 cells with the CYP3A4 inhibitor, ketoconazole, inhibited the AFB1-induced cytotoxicity and micronucleus formation in TK6 cells, suggesting that intestinal metabolism is involved in the AFB1 genotoxic response in TK6 cells. Our results suggest that the Caco-2/TK6 co-culture model is suitable for modelling the role of intestinal biotransformation and transport processes in the genotoxic potential of oral drugs and food contaminants in target blood cells.