Farnesoid X receptor (FXR), a bile acid receptor, serves as a member of the nuclear receptor superfamily. It plays a pivotal role in regulating hepatic inflammation and regeneration. Recent evidence suggests, that FXR and the bile acid are involved in diseases such as cholestatic and inflammatory liver diseases, hepatocellular carcinoma, and bacterial translocation. In this review we discuss the pathophysiology influence of FXR and the bile acid on liver, biliary and gastrointestinal diseases and its mechanisms.