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Objective: To assess the effect of foot and mouth disease (FMD) vaccination on seminal and biochemical profiles of semen of mithun at pre and post vaccinated stage. Methods: The breeding bulls were maintained at Semen Collection Centre, National Research Centre on Mithun, Jhapani, Nagaland. A total of 160 ejaculates were collected from eight mithun bulls twice a week at about 4 weeks in pre vaccinated stage and 12 weeks post vaccinated stage to know the effect of vaccine stress on seminal and biochemical profiles of mithun semen. The vaccine was given at the end of 4th week of experimental period and semen was collected and evaluated upto the 16th weeks of experimental period. Results: It revealed that FMD vaccination affected the sperm functional and biochemical parameters significantly (P<0.05) upto 10th weeks of vaccination. But the animal recovered slowly in both physical health and spermiogram.Conclusions:The adverse effect of vaccination on seminal parameters suggest that the semen collection and preservation should be suspended till 10th weeks of vaccination to get normal fertility of sperm to avoid the failure of conception from artificial insemination using such semen in this precious species.