This article studies supply chain consequences from applying the new-more socially acceptable -strategy of emergency vaccination instead of the large-scale killing of healthy animals for controlling livestock epidemics. We consider an outbreak of foot and mouth disease in a densely populated livestock area of the Netherlands. From an epidemiological perspective, simulation results show that emergency vaccination significantly reduces the size of an epidemic, both in terms of the length of an outbreak and in the number of animals killed. However, in a worst-case situation, not destroying the vaccinated animals after the end of the epidemic leads to additional consequential losses for food supply chains involved of about Euro 200 million. A business case illustrates that the exact size of these losses depends on specific supply volumes and marketing strategies. Calculations provide a basis for addressing cost sharing issues and loss reducing opportunities of new responses to livestock epidemics.