Quarantine protocols are a critical component of equine management, designed to prevent the spread of infectious diseases and ensure the health and safety of horse populations.

Quarantine involves isolating horses for a specified period to monitor for signs of illness. This allows for the detection of diseases that may not be immediately apparent, protecting other horses from potential infection.

Whether introducing a new horse to a stable, returning from a competition, or dealing with a disease outbreak, maintaining a proper quarantine area and following biosecurity protocols is essential.

Quarantine plans must take into consideration the layout of the farm, accessibility of resources, types of horses on the property, and many other factors.

Horse farms, boarding facilities, and show facilities should work with a local veterinarian to develop an appropriate quarantine plan for their facility.

When to Quarantine

Quarantine refers to the practice of separating infected or potentially infected animals to reduce the risk of disease spread to other healthy horses on the farm. [1]

Quarantine is strongly recommended when: [1]

  • New horses are introduced to the property
  • Horses return from events, shows, or competition
  • A horse on the property is diagnosed with an infectious disease

The main feature of quarantine is complete separation of quarantined animals from healthy horses by physical barriers or distance, to prevent contact that may transmit disease.

Actively infected horses require a higher level of quarantine protocol that includes additional measures, such as personal protective equipment for handlers.

Quarantine is a critical component of an infectious disease outbreak response plan to prevent infection of healthy animals. All horse facilities should have a quarantine plan in place to rapidly respond to a potential disease threat.

Quarantine for Healthy Horses

Horses can carry many infectious diseases without showing symptoms, allowing them to introduce the disease to other horses before a risk is noted. [2]

Shedding (spreading of infection) without showing obvious symptoms can occur when a horse: [3]

  • Acquires an infection, but the disease is in the incubation period (the period between infection and presenting symptoms)
  • Recovers from an illness but the infection has not completely cleared
  • Symptoms of infection are very subtle

For these reasons, any new horse on a property or horses returning from an event should be quarantined to protect the health of other horses on the farm. [4]

Quarantine for Sick Horses

Horses with a known infectious disease also require quarantine to minimize spread to healthy horses. [3]

Common equine infections requiring quarantine include: [2]

After diagnosis, veterinarians typically advise owners on whether quarantine is necessary.

Signs of Infectious Disease

It’s important for horse owners to familiarize themselves with symptoms of infectious disease so they can take quarantine actions as soon as infection is suspected.

Common symptoms that indicate a potentially infectious disease include: [4]

Quarantine Protocols

The level of quarantine necessary depends on the scenario and the horse’s medical history. [4] There are two main types of quarantine: separation and isolation. [3]


Separation is most common for healthy horses. [3] In this type of quarantine, the goal is preventing direct horse-to-horse contact that may spread disease by placing a physical barrier or distance between individuals. [3]

The most common separation strategy is having segregated sections of the barn or property designated for different types of horses. [3]

For example, pregnant mares may have a separate barn from show horses, to reduce the risk of show horses bringing home a disease that could cause abortion. [3] Some farms also have designated paddocks for new arrivals. [3]

New horses and returning horses should be separated from at-risk horses for 2-3 weeks. [5]

Key features of a separation protocol include: [3]

  • Physical barriers or distance between groups of horses
  • Designated personnel who only contact a particular group of horses
  • Designated equipment for each group
  • Control of equipment, machinery, and vehicle movement between the different groups
  • Separate disposal of manure for each group


Isolation is a stricter quarantine protocol used for horses suspected or known to have an infectious disease. [3] Since these horses are actively releasing infectious material, isolation protocols aim to reduce transfer of infectious material out of the isolation zone. [3]

Isolation areas have the same features as separation, with additional requirements to further contain disease. [3]

Additional features of isolation areas include: [3]

  • Demarcation of the isolation area using tape, flags, or other visual identifiers
  • Visible signs indicating that quarantine protocols are in effect
  • Personal protective equipment (PPE) for all handlers
  • A designated area for applying and removing PPE and washing hands
  • Footbaths or disposable foot covers at the entrance to the isolation area
  • Disinfection and cleaning protocols at regular intervals
  • Restriction on all equipment, machinery, vehicle, and animal movement through the area
  • Logbooks recording all individuals entering and leaving the isolation area

Personal Protective Equipment

Personal protective equipment requirements can vary depending on the disease involved, whether handlers must manage healthy horses on the same day, and other factors. [3] Whether disposable or reusable PPE is appropriate also depends on these factors. [3]

PPE may include: [3]

  • Gloves
  • Face masks
  • Face shields
  • Boot covers
  • Coveralls, smocks, or gowns
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All farms with livestock should have a quarantine plan prepared in advance. Equine facilities should work with their veterinarian to develop a plan that is suitable for their property layout, resources, and types of horses present in their herd. [3]

When developing a quarantine protocol, there are several considerations to ensure smooth implementation. A robust plan should detail each of these considerations, and any staff involved in handling horses need comprehensive training. [3]


The quarantine plan should detail a specific location on the farm for quarantined animals. [5] This location should be as far away as possible from typical farm traffic, including people, other horses and animals, and vehicle traffic. [5]

At a minimum, the quarantine area requires: [5]

  • A well-demarcated perimeter to restrict unnecessary traffic through the area, such as tape on the floor, flags on a rope, lunge lines, caution tape, etc.
  • Signs surrounding the perimeter indicating that it is a quarantine area
  • Easy access to large machinery, in the case of death or a down horse
  • A distance of at least 5 meters (16 feet) between the quarantine area and other horses

Ideally, a quarantine stall or area should have non-porous flooring, such as concrete. [5] This allows for easy cleaning and disinfection after the quarantine period is over. [5]

Suggestions for quarantine locations include:

  • The last stall at the end of a barn aisle, which can be blocked off easily to restrict access
  • The paddock furthest from the barn, out of the way of normal horse traffic routes
  • Temporary fence panels to make a stall or paddock in a preferred location

Water and Feed Sources

When choosing a quarantine location, it is important to consider the feed and water sources available in that location. Quarantine areas should have separate waterers and forage sources from other horses. [4]

Waterers or hay feeders shared across fence lines are not suitable for quarantine use, unless the other paddock or pasture area is empty.

Additionally, quarantined horses should not be turned out on pastures used for other horses, even if the horses do not come into direct contact.

Ideas for water and feed sources for quarantine areas include:

  • Designated water tubs or troughs filled with a water hose that is not used for filling other horses’ water troughs
  • Designated hay nets clearly marked as quarantine use only
  • Feeding small square hay bales or hay cubes that are easily portioned versus feeding a round bale

Manure Disposal

Another consideration for a quarantine area is disposal of manure and other wastes from the area. The manure from a quarantine area should have its own disposal location, separate from manure disposal from healthy horses. [3]

Farm owners should consider the pathway that wheelbarrows or vehicles used for manure disposal will take to the disposal location. This pathway should be included within the quarantine area, which may disrupt normal operation of the farm. [3]

For isolation areas, stricter protocols for manure disposal are necessary. [5] Generally, veterinarians recommend placing manure and waste in heavy plastic bags or covered dumpsters for direct disposal in a landfill. [5] This reduces the risk of disease exposure associated with open-air manure piles or spreading waste on pastures. [5]

Additionally, an ideal quarantine area should have no run-off of urine or manure into a location that healthy horses can access. [5] Farm owners should consider the gradation of land for outdoor quarantine areas, and the placement of drains for indoor areas.

PPE Stations

There should be a designated area for putting on and taking off PPE items in the vicinity of the quarantine area. [5] Having two separate areas, one for donning PPE and one for removal, is ideal for reducing the risk of cross-contamination. [5]

When planning a PPE station, farm owners should consider the location of several key features: [5]

  • Footbaths or mats at the entrance and exit of the PPE area
  • Handwashing or hand sanitizer stations
  • Storage for gloves, gowns, boots, and other PPE items
  • Changing area for handlers
  • Disposal of PPE items such as gloves or disposable gowns
  • Laundry baskets for reusable gowns and similar items

Care Equipment

Quarantined horses require their own set of care equipment that is not shared with any groups of healthy horses. [5] Equipment used within the quarantine area should have clear labelling, such as a strip of colored tape. [5]

The equipment necessary for managing quarantined horses depends on the farm and the farm layout.

Common items include: [5]

  • Halters and lead ropes
  • Feed tubs
  • Water buckets
  • Pitchforks
  • Wheelbarrows
  • Twitches
  • Oral syringes
  • Thermometers
  • Grooming supplies
  • Bandage materials

Any equipment shared between quarantined horses should be thoroughly disinfected between uses. [5] Performing any cleaning or laundering of these items in an area with low traffic and on an easily disinfected surface (such as concrete) is ideal. [5]

Pest and Insect Control

Many infectious diseases that cause outbreaks spread by contact with a contaminated environment. [5] Pests, such as rodents, can carry infectious diseases on their skin and fur. [5] This can result in spread of the disease to other areas of the farm, even with proper quarantine protocols. [5]

Additionally, several diseases can spread through insect bites, including bites from mosquitoes or midges. [5] Insect control strategies are an important component of a quarantine plan, particularly in isolation scenarios involving a known insect-transmitted disease. [5]

Strategies to reduce pest and insect exposure include: [4][5]

  • Storing feed in rodent-proof bins
  • Removing brush and tall grasses in the area
  • Using baited traps to remove or relocate rodent populations
  • Cleaning up any spilled feed and manure as soon as possible
  • Removing areas of standing water or mud
  • Applying insecticides under the guidance of a trained professional
  • Using insect repellents on all horses on the farm
  • Using fly masks, leg boots, and fly sheets on all horses on the farm

Cleaning and Disinfection

Cleaning and disinfection is a critical component of a well-managed quarantine area. Different disinfectants are effective against different types of infectious agents (pathogens) and have different application processes and times. [5]

Farm owners should consult with their veterinarian to determine the best disinfectant for their quarantine area. [5] Common disinfectants used on horse farms include: [2][6][7]

Disinfectant Category Example Product Effective Against Notes
Phenolic compounds
  • 1-Stroke Environ®
  • Tek-trol®
  • Bacteria
  • Viruses
  • Fungi
  • Inactivated by hard water
  • Lethal to cats
  • Clorox®
  • Bacteria
  • Viruses
  • Inactivated by organic matter
  • Unstable when exposed to light
  • Hazardous when mixed with detergent
Quaternary ammonium compounds
  • Quatsyl®
  • Bacteria
  • Viruses
  • Inactivated by hard water and organic matter
Iodine compounds
  • Betadine
  • Bacteria
  • Viruses
  • Fungi
  • Inactivated by organic matter
  • Isopropyl alcohol
  • Bacteria
  • Some viruses
  • Fungi
  • Flammable
  • Hibitane®
  • Bacteria
  • Viruses
  • Inactivated by organic matter
Peroxygen compounds
  • Prevail®
  • Virkon®
  • Bacteria
  • Viruses
  • Effective even in presence of organic matter


Always inform your veterinarian of which animals may be exposed to disinfectants before choosing chemicals for your operation. Some animals are highly sensitive to disinfectants, especially cats.


Cleaning of Housing Areas

During quarantine, handlers should thoroughly clean and disinfect all housing areas and equipment between horses. [5] The quarantine plan should have set guidelines on the frequency and method of cleaning used in a particular quarantine area. [5]

Stalls, paddocks, or pastures with dirt floors are extremely difficult to clean and disinfect, as organic materials such as dirt and manure inactivate most disinfectants. [5] Farm owners should consider the types of surfaces present in their quarantine area, and be aware that complete disinfection of some surfaces is impossible. [5][7]

To clean stalls with concrete or other hard surfaces on the walls and floors: [5][7]

  • Wet down all of the surfaces with a cleaning detergent and water
  • Let the surfaces soak for 5-10 minutes to allow softening of dried dirt and manure
  • Scrub surfaces with a stiff-bristled broom or brush
  • Rinse all surfaces using a low-pressure hose nozzle
  • Allow the stall surfaces to dry before applying a disinfectant following label directions

To clean stalls with dirt or clay flooring, or porous materials such as untreated wood: [5]

  • Remove all bedding and a layer of flooring material
  • Dry scrub all surfaces to remove as much dirt and manure as possible
  • Scrub the stall walls with a detergent solution
  • Let the surfaces dry before applying a disinfectant solution


Quarantine protocols reduce the risk of disease spread from infected or potentially infected horses.

  • New horses, horses returning from events, and sick horses require quarantine
  • All horse facilities should have a quarantine plan in place, developed under the guidance of a veterinarian
  • The level of quarantine measures necessary depends on the disease threat
  • Quarantine plans must be specific for the farm or facility and take into consideration factors like layout, resource accessibility, and types of horses on the property

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  1. Traub-Dargatz, J. L. et al. An Overview of Infection Control Strategies for Equine Facilities, with an Emphasis on Veterinary Hospitals. Veterinary Clinics of North America: Equine Practice. 2004.View Summary
  2. Dwyer, R. M. Environmental Disinfection to Control Equine Infectious Diseases. Veterinary Clinics of North America: Equine Practice. 2004.View Summary
  3. Sellon, D. C. and Long, M. T., Eds. Equine Infectious Diseases. Second edition. Saunders/Elsevier, St. Louis, Missouri. 2013.
  4. Equine Biosecurity Principles and Best Practices. Alberta Equestrian Federation.
  5. General Biosecurity Guidelines. American Association of Equine Practitioners. 2022.
  6. Personal Hygiene and Disinfectants around Horse Barns. Ontario Ministry of Agriculture, Food and Rural Affairs. 2022.
  7. Dwyer, R. M. Disinfecting Equine Facilities. Revue scientifique et technique – Office international des épizooties. 1995.