Animal protection related to the control of infectious diseases is a complex issue. In case of such a threat, two types of legal goods are in conflict – the life and health of people and animals, protected against the spread of an infectious disease and the related threats, and freedom of animals from pain or suffering. Due to the potentially occur widely spread of a contagious disease of animals within epizootic, the killing is often the only chance to discontinue epizootic chain and arresting further development of the disease. Consequently, the legislator gives higher priority to the safety of the health of people and animals arriving on a specific territory in connection with the threat that the epizootic area than to welfare of the individual animals. However, it is unacceptable to completely abandon all aspects of the humanitarian protection of animals. Justified by an epizootic, killing an animal does not eliminate the need for such operations to be carried out humanely.