Keeping Your Horse Healthy: A Guide to Yearly Vaccinations and Checkups

We just had our annual Spring Health Day here yesterday. Part of good horse husbandry is keeping our horses vaccinated. Not all horses here leave the farm, but we still need to protect them from anything the other horses could bring home from the various clinics and shows we attend.

Routine vaccinations and examinations are not just about disease prevention—they’re about longevity and quality of life. A horse that receives regular veterinary care is less likely to suffer from preventable illnesses and will perform better in competition, and daily activities.

As a responsible horse owner, keeping your equine partner healthy and thriving is a top priority. Here’s everything you need to know about annual shots and examinations for your horse.

Annual Vaccinations: What Your Horse Needs

Vaccinations are a crucial part of equine health care, helping to prevent infectious diseases that can be costly and even fatal. The American Association of Equine Practitioners (AAEP) categorizes vaccines into core and risk-based groups.

List of Vaccines - Deep Dive below

Core Vaccinations (Recommended for All Horses)

These vaccines are essential for every horse, regardless of location, lifestyle, or exposure level:

• Tetanus: Protects against Clostridium tetani, a bacterium found in soil that causes muscle spasms and paralysis.

• Eastern & Western Equine Encephalomyelitis (EEE/WEE): Mosquito-borne viruses that affect the nervous system and can be fatal.

• West Nile Virus (WNV): Another mosquito-borne disease that causes neurological symptoms and can be deadly.

• Rabies: A fatal disease that can be transmitted to humans, making vaccination crucial for both equine and human health.

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Risk-Based Vaccinations (Administered Based on Exposure)

Some horses require additional vaccines depending on their environment, travel frequency, and exposure risk. Discuss with your veterinarian whether your horse needs:

• Equine Influenza: Important for horses that travel or interact with others frequently.

• Equine Herpesvirus (EHV-1 & EHV-4): Also known as rhinopneumonitis, affecting respiratory health and potentially leading to neurological disease.

• Strangles: A contagious bacterial infection that causes swollen lymph nodes and respiratory distress.

• Potomac Horse Fever: Common in areas with standing water, leading to fever, diarrhea, and laminitis.

• Botulism: Recommended for horses fed high-risk feeds like round bales.

Deep Dive Into Core Vaccines

Tetanus

Tetanus is a bacterial infection caused by Clostridium tetani, a bacterium commonly found in soil, manure, and rusty metal. Horses may sustain puncture wounds, scrapes, or surgical incisions where the bacteria can enter. Once inside the body, C. tetani produces a potent neurotoxin that attacks the nervous system, leading to muscle stiffness, spasms, and difficulty eating or moving. Without treatment, tetanus can cause severe paralysis and may be fatal.

The tetanus vaccine is highly effective and provides strong protection against this painful and life-threatening disease. Horses typically receive a tetanus toxoid vaccine annually, though a booster is recommended if a horse suffers a deep wound or undergoes surgery. Because tetanus has no cure once symptoms appear, prevention through vaccination is critical. Horse owners should also ensure that wounds are cleaned promptly and that tetanus boosters are administered as needed.

Eastern/Western Equine Encephalomyelitis (EEE/WEE)

Eastern and Western Equine Encephalomyelitis (EEE and WEE), sometimes just referred to as East West, are viral diseases transmitted by mosquitoes that primarily affect the nervous system. EEE is more common in the eastern and southeastern United States, while WEE is more prevalent in the western and central states. These viruses infect the brain and spinal cord, causing neurological symptoms such as fever, depression, loss of coordination, seizures, and paralysis. EEE has a mortality rate of up to 90%, making it one of the most fatal equine diseases, whereas WEE is slightly less deadly but still highly dangerous.

Vaccination is the best defense against EEE and WEE, as there is no specific treatment once a horse is infected. Horses should receive an initial series of vaccines followed by annual boosters, typically in the spring before mosquito season begins. In areas with high mosquito populations, some veterinarians recommend biannual vaccinations. Along with vaccination, reducing mosquito exposure through fly sheets, fans, and insect repellents can further lower the risk of infection.

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West Nile Virus (WNV)

West Nile Virus (WNV) is another mosquito-borne disease that affects horses, humans, and birds. First identified in the U.S. in 1999, WNV causes inflammation of the brain and spinal cord, leading to neurological symptoms similar to those of EEE and WEE. Infected horses may show signs of muscle twitching, weakness, stumbling, difficulty standing, and, in severe cases, paralysis or death. While some horses recover, neurological damage may be permanent, affecting their long-term performance and quality of life.

The West Nile vaccine is an essential part of equine health care, with annual boosters recommended for all horses. As with EEE and WEE, prevention also involves mosquito control. Keeping horses stalled during peak mosquito hours (dusk and dawn), eliminating standing water, and using fly sprays can help reduce the risk of WNV. Because WNV has no cure, vaccination remains the most effective way to protect horses from this potentially deadly disease.

Rabies

Rabies is a fatal viral disease that affects all mammals, including horses, pets, wildlife, and humans. The virus is transmitted through the saliva of infected animals, usually via bites from rabid skunks, raccoons, bats, or foxes. Once inside the body, the rabies virus attacks the central nervous system, leading to severe behavioral changes, neurological dysfunction, aggression, paralysis, and ultimately death. Because rabies is always fatal once symptoms appear, prevention is the only option.

The rabies vaccine is a core vaccine recommended for all horses. Unlike some other vaccines, rabies requires only a single annual dose to provide protection. Even though horses have a lower risk of exposure compared to dogs or cats, they can still encounter rabid wildlife, especially in rural or wooded areas. Since rabies is a zoonotic disease (transmissible to humans), vaccinating horses also helps protect owners, stable workers, and veterinarians from potential exposure.

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Risk-Based Vaccines

Strangles

Strangles is a highly contagious bacterial infection caused by Streptococcus equi. It primarily affects the upper respiratory tract, leading to swollen and abscessed lymph nodes in the throat and jaw area. Infected horses typically develop a high fever, thick nasal discharge, difficulty swallowing, and swelling around the throat, which can sometimes lead to airway obstruction—hence the name “strangles.” The disease spreads rapidly through direct contact, contaminated water, equipment, or even human handlers.

The strangles vaccine is an important preventative measure for horses that frequently travel, show, or are housed in boarding facilities where exposure risk is high. There are two types of vaccines available: an intramuscular injection and an intranasal spray. The intranasal vaccine is often preferred as it provides localized immunity in the respiratory tract, where the infection begins. While the vaccine does not always prevent infection entirely, it significantly reduces the severity of symptoms. Good biosecurity practices, including isolating new horses and disinfecting shared equipment, are also essential in preventing outbreaks.

Potomac Horse Fever (PHF)

Potomac Horse Fever (PHF) is a bacterial disease caused by Neorickettsia risticii, which infects horses through the ingestion of aquatic insects, such as mayflies and caddisflies. The bacteria target the gastrointestinal tract, leading to severe diarrhea, fever, depression, and in some cases, laminitis. Horses living near rivers, streams, or ponds are at the highest risk, particularly during the warmer months when insect activity increases.

The PHF vaccine is available and can help reduce the severity of the disease, though it does not provide complete immunity. Horses in high-risk areas should receive an annual or biannual booster, depending on their exposure risk. In addition to vaccination, horse owners should take steps to limit standing water near barns and use insect control measures to reduce the number of aquatic insects that could carry the bacteria. Prompt veterinary treatment with antibiotics and supportive care is critical for horses that do contract PHF.

Equine Herpesvirus (EHV-1 & EHV-4)

Equine Herpesvirus (EHV) is a highly contagious virus that affects horses worldwide, with EHV-1 and EHV-4 being the most common strains. EHV-1 can cause respiratory disease, abortion in pregnant mares, and a severe neurological form known as Equine Herpesvirus Myeloencephalopathy (EHM). EHV-4 primarily affects the respiratory system, causing symptoms such as fever, nasal discharge, coughing, and lethargy. Both strains spread through direct horse-to-horse contact, airborne droplets, contaminated surfaces, and even human handlers.

The EHV vaccine is a key tool in reducing the spread and severity of the disease. Horses that travel, compete, or are in boarding facilities should receive the vaccine every six months, while broodmares require specific vaccination protocols to prevent abortion. However, while the vaccine helps prevent respiratory and abortion-related forms of EHV, it does not offer full protection against the neurological form (EHM). In addition to vaccination, strong biosecurity measures—such as isolating new arrivals, disinfecting equipment, and minimizing horse-to-horse contact—are crucial for preventing outbreaks.

Equine Influenza (Flu)

Equine Influenza is one of the most common and contagious respiratory diseases in horses. Caused by influenza A viruses, it spreads rapidly through airborne droplets from coughing or sneezing horses, as well as through contaminated surfaces and equipment. Symptoms include fever, persistent coughing, nasal discharge, and lethargy. While rarely fatal, equine flu can lead to prolonged illness, weight loss, and decreased performance, making it a significant concern for horses in high-traffic environments such as barns, racetracks, and showgrounds. Recovery can take weeks, and secondary bacterial infections may complicate the healing process.

Vaccination is the most effective way to prevent equine influenza, particularly for horses that travel, compete, or are exposed to new horses frequently. The flu vaccine is typically administered twice a year for high-risk horses, while others may receive annual boosters. Because flu viruses can mutate over time, updated vaccine strains are periodically released to match circulating virus variants. In addition to vaccination, reducing stress, maintaining good ventilation, and following strict hygiene practices in barns can help minimize the risk of outbreaks.

Your horse’s annual exam is also a good time to develop a relationship with your vet. You never know when you will have an emergency and need them ASAP.

Annual Veterinary Examination: A Comprehensive Health Check

Beyond vaccinations, an annual veterinary examination helps assess your horse’s overall well-being. A routine checkup typically includes:

1. General Physical Exam

• Checking weight and body condition score

• Evaluating coat, hooves, and muscle tone

• Listening to heart, lungs, and gut sounds

An annual wellness exam is a critical part of maintaining your horse’s long-term health and performance. This comprehensive checkup allows veterinarians to assess the horse’s overall condition, identify potential health concerns early, and develop a customized care plan. Preventative care is always more effective and cost-efficient than treating illnesses or injuries after they occur. A well-managed horse with regular veterinary care is more likely to stay sound, perform better, and have a longer, healthier life. During the wellness exam, the vet will evaluate various aspects of the horse’s health, including teeth, body condition, hooves, and general physical well-being.

In addition to dental care, the vet will assess the horse’s body condition score (BCS), which helps determine if the horse is underweight, overweight, or at an ideal weight. Monitoring BCS is crucial for managing diet, workload, and overall health.

2. Dental Health Assessment

• Examining teeth for sharp points or uneven wear

• Floating teeth if necessary to ensure proper chewing and digestion

One of the most important aspects of the annual wellness exam is checking the horse’s teeth. Horses' teeth grow continuously, and uneven wear can lead to sharp points, difficulty chewing, and even weight loss. A veterinarian will perform a dental exam to look for any abnormalities, signs of discomfort, or the need for floating (filing down sharp edges). Proper dental care ensures that horses can chew their food efficiently, which is essential for digestion and nutrient absorption

3. Parasite Control & Fecal Testing

• Conducting fecal egg counts to determine parasite load

• Creating a deworming plan based on the test results

Parasite control is an essential part of maintaining a horse’s overall well-being, as internal parasites can cause serious health issues such as weight loss, colic, poor coat condition, and digestive disturbances. Common equine parasites include strongyles, roundworms, tapeworms, and bots, all of which can damage the horse’s intestines and weaken the immune system.

A crucial part of an effective parasite control program is conducting fecal egg counts (FECs), which help determine the parasite load in an individual horse. This simple test involves analyzing a manure sample to measure the number of parasite eggs present, allowing veterinarians to identify horses with high parasite burdens that require treatment.

Low shedders, or horses with minimal parasite loads, may not need frequent deworming, while high shedders may require a more targeted approach. In addition to deworming, proper pasture management—such as regular manure removal, rotational grazing, and avoiding overcrowding—can help reduce parasite exposure.

4. Coggins Test & Health Certificates

• Testing for Equine Infectious Anemia (EIA), required for travel and boarding

• Issuing health certificates if your horse will be transported across state lines

Read our article for a deep dive into why you should get a coggins test

5. Hoof & Lameness Evaluation

• Checking for early signs of lameness or joint issues

• Discussing farrier care and corrective shoeing if needed

Hoof care is another essential component of the wellness exam. The veterinarian will inspect the hooves for cracks, thrush, abscesses, or signs of laminitis, ensuring that the horse is receiving appropriate farrier care. Regular trimming or shoeing is vital to maintaining soundness and preventing lameness.

Author, Ame Vanorio, is the director of Fox Run Environmental Education, an author, and horse mom to Rocket.