BackgroundEndogamy increases the risk of manifestation of deleterious recessive genes. Mitochondrial DNA allows the separation of American Zebu (Bos indicus and Bos taurus) and evaluate the effect of mitochondrial DNA on productive traits of cattle. However, the effect of endogamy and mitochondrial DNA (mtDNA) on the immune system remains unclear. The aim of this study was to evaluate the association between endogamy, mtDNA and immune parameters.ResultsA total of 86 cattle (43 cows and 43 calves) were used in this study. Age, endogamy, milk yield, and origin of mtDNA were measured and their influence on immunological parameters was evaluated. Older cows had increased CD4+ T cells, decreased CD21+ and γδhigh T cells as well as increased CD4+/CD8+ and T/B ratio. Multiple regression analysis indicated that endogamy in calves was associated with increased CD8+ T and CD21+ B lymphocytes, and decreased γδhigh T cells in peripheral blood. Cows with medium and lower endogamy had a lower percentage of B lymphocytes and γδlow T cells and cows with lower endogamy had higher levels of γδ T cells and γδhigh T cells, as well as the CD4+/CD48+ cell ratio. Calves with higher endogamy had higher levels of CD8+ T lymphocytes, whereas calves with lower endogamy had lower levels of γδlow T cells.ConclusionsThese results demonstrated for the first time that endogamy influences the immune system of cattle.