Equine emergency shelters have an increased risk of infectious disease occurrences due to increased animal stress levels, excessive co-mingling, inconsistent worker base, and horses arriving from many and varied health management and stabling situations. Biosecurity policies should be in place ahead of time to prevent disease spread and outbreak situations and policies should be effectively conveyed to all shelter personnel. A veterinarian should be involved in the overall health management of an equine emergency shelter including working with public health officials regarding the overall animal and human safety issues associated with effectively managing an equine shelter. The veterinarian should work closely with the shelter manager and both need to be able to apply Incident Command System and National Incident Management Systems applications to maximize disease prevention. Mitigation tactics should include appropriate regular equine health maintenance including current vaccinations against tetanus, Equine Influenza I & II, Equine Herpes virus I & IV, and the encephalitides including Eastern, Western, and West Nile Viruses as part of horse owner emergency preparedness planning. Equine Infectious Anemia (EIA) is a federally regulated equine disease and during disaster situations it is unrealistic to assume that all horses will have a record of a current negative test. EIA testing should be considered a part of the plan for shelter animals depending on risk assessments. Appropriate personal hygiene, particularly hand hygiene, can assist in the prevention of disease transmission. Separate isolation areas are necessary for horses showing clinical signs of infectious disease including fever, nasal discharge, or diarrhea. Equine emergency shelter husbandry plans should include a plan for safe handling of feedstuffs, and water. An effective and implementable biosecurity plan for equine emergency sheltering is a key critical requirement for successful large animal emergency and disaster response outcome.