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Bovine leukemia virus (BLV) causes enzootic bovine leukosis, a malignant form of B-cell lymphoma, and is closely related to human T-cell leukemia viruses. We investigated whether BLV infection affects host genes associated with DNA mismatch repair (MMR). Next-generation sequencing of blood samples from five calves experimentally infected with BLV revealed the highest expression levels of seven MMR genes (<i>EXO1</i>, <i>UNG</i>, <i>PCNA</i>, <i>MSH2</i>, <i>MSH3</i>, <i>MSH6</i>, and <i>PMS2</i>) at the point of peak proviral loads (PVLs). Furthermore, MMR gene expression was only upregulated in cattle with higher PVLs. In particular, the expression levels of <i>MSH2</i>, <i>MSH3</i>, and <i>UNG</i> positively correlated with PVL in vivo. The expression levels of all seven MMR genes in pig kidney-15 cells and the levels of <i>PMS2</i> and <i>EXO1</i> in HeLa cells also increased tendencies after transient transfection with a BLV infectious clone. Moreover, MMR gene expression levels were significantly higher in BLV-expressing cell lines compared with those in the respective parental cell lines. Expression levels of <i>MSH2</i> and <i>EXO1</i> in BLV-infected cattle with lymphoma were significantly lower and higher, respectively, compared with those in infected cattle in vivo. These results reveal that BLV infection affects MMR gene expression, offering new candidate markers for lymphoma diagnosis.