Cholangiocarcinoma (CCA) is a malignancy with dismal prognosis that arises from biliary epithelial cells (BECs) lining intra- and extra-hepatic bile ducts. BECs possess antigen presentation capacity and can activate MAIT cells via MR1. MAIT cells are known to be enriched in human liver and locate around bile ducts. Thus, MAIT cells may affect antitumor immune responses in CCA. However, little is known regarding MAIT cell presence and function in tumors. When characterizing MAIT cells in non-tumorous tissues, we noted a specific enrichment of the cells within the biliary tract system. Assessing CCA, the tumor microenvironment was characterized by a retained presence of cytotoxic T cells and high numbers of regulatory T cells. However, a specific loss of MAIT cells was noted within tumors as compared to surrounding non-affected liver tissue. The residual intratumoral MAIT cell population was enriched for cells expressing tissue residency markers but displayed an exhausted phenotype. Intriguingly, the loss of MAIT cells was accompanied by high expression of MR1 within tumors. This expression was primarily confined to myeloid cells suggesting an MR1-dependent mechanism driving the loss and exhaustion of intratumoral MAIT cells. It still remains to be explored whether the residual MAIT cells possess the capacity to target and kill tumor cells and whether such targeting is beneficial for the patients.