As the human animal bond has strengthened, the public has demanded more professional and compassionate care for homeless animals, rejecting the previously held notion that, unfortunately, the only or best solution to the pet overpopulation problem was humane euthanasia. This demand for better care has resulted in unprecedented interest and involvement of the veterinary community in shelter operations. The management of health care for dogs and cats housed in shelters differs in many ways from the methods employed in either private practice or other confinement situations such as kennels or laboratories. Without real data or shelter studies, veterinary professionals must often improvise and extrapolate from the veterinary literature to provide solutions to challenging shelter problems; but it is also becoming increasingly clear that intuitive judgments and traditional health care strategies are often ineffective in shelter settings. The volume of veterinary research regarding shelter medicine has increased in recent years, but some of it has only created more questions, leading to challenges to some of the more widely held beliefs regarding sanitation, stress reduction, ventilation, quarantine and even vaccination protocols in shelters. Clearly more research is needed to enrich the lives of shelter animals.

In order to work effectively with a shelter, it is imperative to understand the mission of the organization. Shelters typically fall into several different categories. They may be municipal shelters or private humane societies. Municipal shelters generally focus on animal control and thus public health protection and managing nuisance complaints. They may be further categorized as open admission facilities that offer a variety of community programs as well. Municipal or open admission shelters must accept all animals that are presented to them regardless of the condition or number of animals already in the facility, and often utilize euthanasia routinely to manage their population numbers and disease. This open admission policy can set the stage for uncontrollable disease transmission, especially if the shelter is already overcrowded, understaffed and must hold animals with obvious or inapparent infectious disease. Private humane societies or societies for the prevention of cruelty to animals (SPCAs) may or may not have the contract to provide animal control services to the community. In addition to offering several of their own animal welfare oriented programs, including spay neuter, behavior counseling, adoptions, etc, they may be known as limited admission, or "no kills" that can close their doors to avoid overcrowding or manage disease. They typically perform some euthanasia, but not as a matter of routine. However, by holding adoptable animals for longer periods in order to find homes, they sometimes extend themselves beyond their capacity to provide humane and adequate care and end up with disease problems. Private organizations and individuals may act as sanctuaries or rescue groups, often operating from the owner's home. None of these entities has an affiliation with an "umbrella" national organization such as the ASPCA or HSUS and there are no federal care guidelines. There are only a few state regulations regarding shelter operations.

Although shelters may have different goals and resources, the overriding mission of all facilities should be to provide a clean, comfortable and safe environment that addresses the emotional and physical needs of the individual animal and minimizes their stress. The control of disease transmission must continually be addressed, recognizing that some disease may be inevitable because of the constant introduction of new animals who are potentially diseased, and the interaction between host, environment and agent factors. Shelter animals are more vulnerable to disease transmission because of their often-debilitated conditions (i.e. they may be stressed, sick, injured, malnourished, parasitized, etc.) and the increased risk of exposure to disease from other animals in the facility. In addition to exposure to sick animals, disease agents may be endemic in a physical environment that may be damp, subject to temperature fluctuations, shoddily constructed or dilapidated, poorly ventilated, difficult to clean and sanitize and overcrowded. Some pathogens (i.e. parvovirus, calicivirus and ringworm spores) can survive for long periods of time in the environment and are also difficult to inactivate; others have carrier states (herpes, calici virus) and shedding periods (parvo) that make disease detection and control difficult. Identification of and a thorough understanding of each pathogen is required to prevent and manage disease outbreaks; in addition to understanding pathogenesis, epidemiology, morbidity and mortality rates, there should be a thorough knowledge about carrier states, shedding periods, modes of transmission, survival rates in the environment, which chemicals can inactivate and so on.