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The liver contributes to immune surveillance against pathogens entering via the gut and is itself influenced by alterations in mucosal immune responses and the microbiome. Mucosal immunity is also implicated in autoimmune liver diseases that associate with inflammatory bowel disease (IBD), and in steatohepatitis where compromised enteric barrier function and altered bacterial sensing drive liver inflammation. In this article, we discuss recent advances in our understanding of how dysregulated mucosal immune responses result in hepatobiliary injury; specifically through defective intestinal barrier function, changes in the enteric microbiome and loss of immune tolerance, and via shared leucocyte recruitment pathways.