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Creating A Vaccination Program For Horses At Your Animal Sanctuary

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Veterinary Review Initiative
This resource was reviewed for accuracy and clarity by a qualified Doctor of Veterinary Medicine with farmed animal sanctuary experience as of October 2025.

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A Note For Readers From Outside Of The US
Whenever possible, we strive to create resources that can serve the global sanctuary community, but some topics require a more specific focus. While folks caring for horses outside of the US can still gain important information from this resource, we do want to point out that it is focused on vaccine recommendations in the US. Because disease risk can vary by geographical location, and vaccine availability and regulations differ from country to country, some of the information below may not apply to horses outside of the US.

Vaccines can play an important role in helping to keep residents healthy, but it’s important to work with your veterinarian to establish the most appropriate vaccine protocols based on the specifics of your resident population and your region. You can read a bit more about working with your veterinarian to establish a vaccination program for your residents here. Even though many vaccines can be purchased and administered without a veterinary license, veterinary involvement is crucial! Some vaccinations are considered “core” vaccines, meaning they are recommended for all horses unless there is a medical reason not to vaccinate. However, there is no universally recommended standard vaccination program for horses. When determining the most appropriate vaccination program for your horse residents, your veterinarian will consider their risk of disease, the consequences of disease, and the safety and efficacy of available vaccines. 

In addition to consulting with your veterinarian regarding which diseases you should vaccinate against, also be sure to consult with them regarding which specific products to use. In some cases, both inactivated and modified live vaccines are available. Additionally, some of the vaccinations described below are available as monovalent vaccines, which offer protection against a single disease or pathogen, while others are available as combination products that offer protection against multiple diseases/pathogens. Your veterinarian will be able to recommend the most appropriate product(s) for your residents. We also recommend talking to them about whether or not they think it is appropriate for you or other caregivers to administer vaccinations, or if they feel it’s safest if they administer them. If you opt to have sanctuary personnel administer vaccines, be sure to follow label instructions (or your veterinarian’s recommendations) regarding any age restrictions, the frequency of boosters, and how to reduce the risk of adverse side effects (as well as what signs to look for that could indicate an adverse reaction and how to respond). Your veterinarian can also offer guidance regarding whether or not multiple products can be administered on the same day or if they should be spaced out (how to best space them out).

The Benefits Of Having Your Veterinarian Administer Vaccinations
While it may seem cheaper and logistically easier to have sanctuary personnel administer vaccines, the American Association of Equine Practitioners (AAEP) points out that there are numerous benefits to having vaccines administered by a veterinarian. These include ensuring vaccines are properly stored, handled, and administered, which will reduce the risk of vaccine failure and adverse reactions. Having your veterinarian administer vaccines also allows for a pre-vaccination examination to ensure the individual is currently healthy enough for immunization. Adverse reactions (ranging from mild to severe) are possible any time a vaccination is administered, even if they are administered by your vet. However, having your veterinarian administer the vaccine means they will be on hand if your resident has an immediate reaction (such as anaphylaxis) and will have the tools and knowledge necessary to appropriately respond. Additionally, if there is a complication with a veterinarian-administered vaccine or if the vaccine fails to provide the protection it should, the drug company may cover treatment costs (but this is not typically the case if the vaccine was administered by someone other than a licensed veterinarian).

Ongoing Communication Is Key, Particularly If Sanctuary Personnel Are Administering Vaccines
If you decide to have sanctuary personnel administer vaccines (after working with your veterinarian to establish vaccine protocols), ongoing communication is key. Just as there is no standard vaccine program that is appropriate for all horses, vaccine protocols that work for most of your residents may not be appropriate for everyone. For example, certain vaccinations may not be recommended for horses who are ill or on certain medications, and if you are caring for a pregnant resident, certain vaccinations may need to be timed carefully to provide protection to their foal.

While an appropriate vaccination program can help minimize the risk of certain diseases, it is just one aspect of disease prevention. Biosecurity, diet, housing, cleaning practices, and veterinary care (amongst other things) also play a crucial role in keeping residents healthy. Below, we’ll offer general information about some of the vaccines that tend to come up most often when caring for horses in sanctuary spaces in the US, including whether or not they are considered a core vaccine by the AAEP. However, as stated above, you should always defer to your veterinarian for specific recommendations for your residents. They may strongly recommend additional vaccines that are not listed here based on the diseases that are prevalent in your area.

A Note On Miniature Horses
According to the AAEP, there is limited data regarding the use of vaccines in miniature horses (as well as mules, donkeys, and zebras). While you should defer to your veterinarian regarding all vaccination protocols, if you care for miniature horses, be sure to talk to them specifically about vaccination protocols for miniature horses. They may make different recommendations for them than for your other horse residents.

Tetanus (Core Vaccine)

Tetanus is a non-communicable, often fatal disease caused by neurotoxins produced by the spore-forming bacterium Clostridium tetani. These organisms are ubiquitous in the soil and can also be found in the intestinal tract and feces of horses and other animals. Infection occurs when C. tetani enters the body via things like puncture wounds, lacerations, surgical incisions, or the open umbilicus of foals. Following administration of the initial vaccination series, the AAEP recommends that horses be revaccinated annually. Revaccination is also recommended if a horse sustains a wound or needs to undergo surgery and has not been vaccinated in the last 6 months.

Eastern And Western Equine Encephalomyelitis (Core Vaccines)

Eastern Equine Encephalomyelitis (EEE) and Western Equine Encephalomyelitis (WEE) are vector-borne diseases transmitted most often by mosquitoes. Following the initial vaccination series, the AAEP recommends at least annual revaccination. Your veterinarian may recommend more frequent vaccination for individuals who are high-risk or who have limited immunity. Because EEE and WEE are vector-borne diseases, revaccination should be done before the vector season begins in the spring. Your veterinarian will be able to make specific recommendations regarding the most appropriate timing.

Venezuelan Equine Encephalomyelitis
Venezuelan equine encephalomyelitis (VEE) is another vector-borne disease that can affect horses. Endemic in parts of Central and South America, VEE is a reportable foreign animal disease in the US. Unlike EEE and WEE, which are core vaccines recommended for all horses (barring a medical reason not to vaccinate), vaccination against VEE is risk-based. Your veterinarian will consider various factors, including your horse resident’s risk of exposure, when determining if VEE should be included in your vaccination protocols.

West Nile (Core Vaccine)

Like EEE, WEE, and VEE, West Nile is also a vector-borne disease. Transmitted primarily by mosquitoes, the virus that causes this disease has been found in each state in the continental US, as well as in Canada, Mexico, and parts of Central and South America. Following the initial vaccination series, annual revaccination is recommended, though your veterinarian may recommend more frequent revaccination. As with vaccination against EEE and WEE, revaccination should be done prior to the start of the vector season in the spring. 

Rabies (Core Vaccine)

The incidence of rabies in horses is low. However, because rabies is almost always fatal and is also zoonotic, the AAEP recommends vaccination against this disease annually. Unlike some other vaccine products, in many states, only a licensed veterinarian can administer rabies vaccines. Proper recordkeeping is imperative when residents receive any vaccination, but this is especially important when it comes to rabies. Be sure to record the date the vaccine was administered as well as the vaccine brand and serial number. When possible, ask the administering veterinarian for documentation for your records. This way, you’ll have proof of vaccination in the event one of your residents is exposed to rabies.

Equine Herpesvirus (Rhinopneumonitis)

Equine Herpesvirus types 1 and 4 (EVH-1 and EVH-4, respectively) are ubiquitous viruses worldwide. EVH-1 and EVH-4 cause varying degrees of respiratory illness, and previously infected individuals often remain asymptomatic carriers who may shed the virus during periods of stress, contributing to disease spread. EVH-1 can also cause neurologic disease and outbreaks of abortion. Currently, the available vaccines do not claim to protect against neurologic disease caused by EVH-1. Your veterinarian will assess your residents’ risk of clinical disease from EVH when making vaccination recommendations. EVH-1 and EVH-4 are endemic in many horse populations, and repeated natural infections lead to the development of some degree of immunity in mature horses. Therefore, your veterinarian may make different recommendations based on the age of each resident. Immunity from vaccination is short-lived, so if vaccination is recommended, your veterinarian may recommend revaccination every 6 months following the initial series.

Strangles (Distemper)

Caused by the highly infectious bacterium Streptococcus equi subspecies equi (S. equi), strangles is a respiratory disease characterized by swelling and possible abscessation of the lymph nodes. It is one of the most common infectious diseases of horses globally. Horses of any age can be affected, but it is most common in younger individuals. Your veterinarian may recommend vaccinating your residents against strangles annually if they are at high risk of exposure or if strangles has been a persistent issue in the past. The risk of adverse reaction is significantly higher in individuals who have been exposed to S. equi. Therefore, your veterinarian may recommend antibody testing prior to administering the vaccine to identify individuals at risk of complications.

Equine Influenza

Like strangles, equine influenza is one of the most common respiratory diseases of horses. Caused by the highly contagious orthomyxovirus equine influenza A type 2 H3N8 subtype, equine influenza is endemic in equines in the US, as well as in equines in much of the rest of the world. If vaccination is recommended for your residents, they will need to be revaccinated every 6-12 months following their primary vaccination series. Your veterinarian will be able to make specific recommendations based on your residents’ risk of exposure.

Potomac Horse Fever

Potomac Horse Fever (PHF) is a bacterial disease believed to be caused by ingestion of infected aquatic insects (such as mayflies and caddisflies) and is associated with pastures that border creeks or rivers, where horses are most likely to ingest these insects. PHF is a seasonal disease that typically occurs between late spring and early fall. Vaccination against PHF is not fully protective against disease but can reduce the severity of clinical signs. If your veterinarian determines your residents to be at risk of PHF, they may recommend including vaccination against PHF in your care protocols. Because of the seasonal nature of this disease, vaccination should be timed to provide the most protection during times of highest risk. Your veterinarian can make specific recommendations about the timing of vaccination and how often to revaccinate.

Botulism

Botulism is caused by potent neurotoxins released by Clostridium botulinum, a ubiquitous bacterium found in the soil. Of the numerous toxins, three have been reported to cause clinical disease in horses in the US: A, B, and C. Of these, type B accounts for more than 85% of clinical cases and is typically found in the soil in the Northeast and Appalachian regions. A vaccine is available that offers protection against type B, which your veterinarian may recommend annually if you live in an area where botulism from type B is endemic. Horses fed round hay bales or large square bales are at an increased risk of botulism, and therefore, your veterinarian may recommend vaccination if this is the type of hay you provide. There is currently no licensed vaccine available that offers protection against types A or C.

Leptospirosis

Leptospirosis is a contagious disease caused by a group of bacteria called Leptospira. Of the many species and serovars, Leptospira interrogans serovar Pomona type kennewicki is responsible for the majority of cases of clinical disease in horses in North America. This bacterium is known to cause three syndromes in horses: acute renal failure, in-utero infection, and Equine Recurrent Uveitis (ERU). If you live in an endemic area, your veterinarian may recommend annual vaccination against this disease. 

Lyme Disease

Lyme disease is caused by Borrelia burgdorferi, a bacterium transmitted by the Ixodes tick (also known as the blacklegged tick or deer tick). In areas where Ixodes ticks are endemic, infection with B. burgdorferi is common. However, following infection, it is not known what percentage of horses will develop Lyme disease. There is currently no vaccine approved for use in horses, but in areas where Ixodes ticks are endemic, some veterinarians recommend off-label use of a canine Lyme vaccine, and according to the AAEP, there is reasonable evidence to suggest the canine vaccine is at least partially protective.

A Quick Note On Dosing
Because horses range in size depending on their breed and age, caregivers may wonder if smaller individuals require smaller doses than other horses. The answer is that they do not. While you may need to wait for a very young foal to reach a certain age before they receive certain vaccinations (following label instructions or your veterinarian’s recommendations), everyone who is eligible for vaccination will receive the same dose as other members of their species, regardless of their weight.

SOURCES:

Vaccination Guidelines | American Association Of Equine Practitioners  

The Science Behind Veterinarian-Administered Vaccines | American Association Of Equine Practitioners 

Vaccine Adverse Reactions | American Association Of Equine Practitioners 

Tetanus Vaccination Guidelines | American Association Of Equine Practitioners 

Rabies Vaccination Guidelines | American Association Of Equine Practitioners 

Eastern & Western Equine Encephalomyelitis Vaccination Guidelines | American Association Of Equine Practitioners 

Mosquito Borne Diseases: Eastern and Western Equine Encephalomyelitis and West Nile Virus – Prevention is Just a Vaccine Away | University Of Connecticut Extension 

West Nile Virus Vaccination Guidelines | American Association Of Equine Practitioners 

Equine Herpesvirus (Rhinopneumonitis) Vaccination Guidelines | American Association Of Equine Practitioners 

Streptococcus equi Infectious Disease Guidelines | American Association Of Equine Practitioners  

Strangles in Horses | Merck Veterinary Manual 

Strangles | UC Davis School Of Veterinary Medicine Center For Equine Health 

Equine Influenza Vaccination Guidelines | American Association Of Equine Practitioners 

Equine Influenza | Merck Veterinary Manual 

Potomac Horse Fever Vaccination Guidelines | American Association Of Equine Practitioners 

Potomac Horse Fever | Cornell University College Of Veterinary Medicine 

Potomac Horse Fever | Cleveland Equine Clinic 

Potomac Horse Fever | Merck Veterinary Manual 

Botulism Vaccination Guidelines | American Association Of Equine Practitioners

Botulism | UC Davis School Of Veterinary Medicine Center For Equine Health 

Botulism | American Association Of Equine Practitioners 

Leptospirosis Vaccination Guidelines | American Association Of Equine Practitioners 

Leptospirosis Guidelines | American Association Of Equine Practitioners 

Lyme Disease In Horses | Cornell University College Of Veterinary Medicine

AAEP Infectious Disease Guidelines: Borrelia burgdorferi infection And Lyme Disease | American Association Of Equine Practitioners

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