Regulations in the United States require animal biosafety level 3 (ABSL-3) or biosafety level 3 agriculture (BSL-3-Ag) containment for many endemic zoonotic pathogens and etiologic agents of foreign animal diseases. In an effort to protect public health, billions of dollars were invested in regulatory programs over many years to reduce the prevalence of zoonotic pathogens such as Brucella and Mycobacterium bovis in domestic livestock. In addition to research needs in domestic livestock hosts, the establishment of brucellosis and tuberculosis in wildlife in the United States has created a need for research studies addressing these zoonotic diseases. As guidelines in the Biosafety in Microbiological and Biomedical Laboratories (BMBL, 2009) for BSL-3 and BSL-3-Ag facilities are primarily directed toward laboratory or vivarium facilities, additional issues should be considered in designing large animal containment facilities for domestic livestock and/or wildlife. Flight distance, herd orientation, social needs, aggressiveness, and predictability are all factors we considered on a species by species basis for designing our containment facilities and for work practices with large ruminants. Although safety risk cannot be completely eliminated when working with large animals, studies in natural hosts are critical for advancing vaccine and diagnostic development, and providing basic knowledge of disease pathogenesis in natural hosts. Data gathered in these types of studies are vital for state and national regulatory personnel in their efforts to design strategies to control or eradicate diseases such as brucellosis and tuberculosis in their natural hosts, whether it is domestic livestock or wildlife. It is likely that failure to address the prevalence of disease in wildlife reservoirs will lead to re-emergence in domestic livestock. The overall benefit of these studies is to protect public health, provide economic benefits to producers, and protect the economic investment made in regulatory programs.