Introduction and Aims: The intestinal epithelium functions to transport nutrients, fluid and electrolytes, while at the same time acting as a barrier to the entry of harmful substances. CFTR is a transmembrane Cl- channel important in regulating intestinal fluid transport and is implicated in the pathogenesis of a number of intestinal diseases. Bile acids, classically known for their roles in lipid digestion, are now also recognised as important enteric hormones that regulate many aspects of epithelial function. Indeed, it is thought that bile acid metabolism is a primary mechanism by which the microbiota communicates with its human host. Here, we set out to investigate the role of the nuclear bile acid receptor, farnesoid x receptor (FXR), in regulating epithelial CFTR expression. Methods: T84 human colonic epithelial cells were cultured as polarised monolayers on permeable supports and treated bilaterally with the FXR agonist, GW4064 (5 μM), over a range of times. Levels of FGF19, an index of FXR activation, CFTR, FXR, FOXA1, and miR-494 were measured by qRT-PCR, western blotting, or ELISA. Results: Treatment of the cells with GW4064 significantly increased FGF19 mRNA expression by 1235 ± 237.3 fold (n = 8; p < 0.05) and protein by 719.6 ± 92.0 pg/mL (n = 5; p < 0.01) after 48 hrs. Moreover, GW4064 downregulated CFTR mRNA to 0.47 ± 0.1 fold after 12 hrs (n = 8; p < 0.01) and protein levels to 0.36 ± 0.1 fold after 48 hrs, compared to vehicle-treated controls (n = 4; p < 0.05). Transcriptomic analysis confirmed FXR-induced downregulation of CFTR in primary human colonic enteroids. Expression of miR-494, which is known to target CFTR, was not increased by GW4064 treatment in T84 cells. However, mRNA expression of FOXA1, a transcription factor that regulates CFTR, was inhibited by 33.2 ± 5.2% after 3 hrs (n = 4; p <0.05). Conclusion: The nuclear bile acid receptor, FXR, regulates colonic epithelial CFTR expression. Such actions are likely to be important in the setting of microbial regulation of host intestinal physiology in health and disease. As such, FXR represents an excellent target for development of new drugs and nutraceuticals to treat intestinal diseases associated with dysregulated CFTR function.