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Shelters should have written policies and protocols in place that detail how medical and behavioral problems will be handled (Hurley 2004). Policies and protocols should be based on research and facts as well as the individual organization's mission, philosophy, and the availability of resources (including facilities, staff, and veterinary care). Policies and protocols are best established by a committee that is responsible for shelter health issues, including the shelter director or manager, medical and behavior staff, and other key individuals. The goals of the committee should be to establish definitions or descriptions of the disease or problem behavior in question, a description of the methods that will be used to diagnose or recognize the condition and a general policy regarding the disposition of animals affected by the condition. In addition, protocols should include details on who should be notified, housing guidelines, sanitation procedures, treatment, and documentation in each case. These written protocols should serve as guidelines for systematic triage and care of animals in the shelter.

In addition to establishing policies and protocols for commonly encountered diseases and problem behaviors of shelter animals, protocols should also be developed to ensure prompt recognition and treatment of pain and emotional distress in animals. Protocols should include provisions for conditions that cause both acute and chronic pain and/or distress. Many shelters receive animals that are victims of cruelty, neglect, and/or trauma; protocols should include provisions for recognition and triage, with the provision of adequate pain control and nursing care as a priority, or emergency euthanasia if necessary when animal suffering cannot be eased, including those in their stray holding period. For shelters that do not have a veterinarian on staff, protocols should contain information for obtaining emergency veterinary care and assistance with cruelty cases.