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Why is my horse coughing?

Equiteca Editorial · Reviewed 2026-09-05 · 4 sources

The short answer

A cough in a horse splits two ways: infection, or the airway reacting to what the horse breathes. Merck describes equine asthma as a chronic, allergen-mediated inflammatory disease of the lower airways covering inflammatory airway disease, recurrent airway obstruction and summer pasture RAO, and puts allergen-induced lower airway inflammation in around 17 percent of mature horses in northern temperate regions, with up to 80 percent of athletic horses affected by mild to moderate asthma at some point in their careers. The University of Florida names mold, organic dust and endotoxin in hay and straw as the most common triggers and says the most important treatment is environmental and dietary management. The other branch is infectious, and that one is about fever and biosecurity: with strangles, Merck puts the incubation period at 3 to 14 days and says the first sign of infection is a fever of 103 to 106 degrees Fahrenheit. Take a temperature before you do anything else.

6 of 6 ranked causes here are pain, not training

On this page (9)
  1. 01The short answer
  2. 02What it looks like
  3. 03Likely causes, ranked
  4. 04What to try
  5. 05When to call the vet
  6. 06Behavior or pain?
  7. 07Questions people ask
  8. 08Keep reading
  9. 09Sources

What it looks like

  • A cough at the start of exercise, on the lunge, or when the horse first puts its head down to hay
  • An intermittent cough at rest, sometimes for weeks
  • Nasal discharge: clear, cloudy, or thick and yellow, from one nostril or both
  • Poor tolerance for fast work, or a horse that has quietly lost its edge
  • Increased breathing rate or visible effort at rest, and flared nostrils
  • A heave line: a ridge along the ribs from thickened abdominal muscle used to push air out, seen in chronic cases
  • Weight loss, poor appetite, or respiratory distress in a severely affected horse
  • Fever, dullness, swollen glands under the jaw, or difficulty swallowing, which point at infection rather than allergy

Likely causes, ranked

A tag marks the causes that are pain wearing a behavior label. Those are the ones to rule out first.

  1. 01Equine asthma from dust, mold and endotoxin in hay and beddingcommonpossible painThe University of Florida names mold, organic dust and endotoxin in hay and straw as the most common allergic triggers for equine asthma, and describes airway narrowing, inflammation, mucus production and bronchospasm. Merck says episodes tend to occur when susceptible horses are stabled, bedded on straw or fed hay, driven by respirable dust including molds, endotoxin, micro-organisms and pollen, and that removing those factors produces remission or a lessening of signs.
  2. 02Mild to moderate asthma showing only as poor performancecommonpossible painMerck describes mild to moderate asthma as nonspecific complaints of poor performance or exercise intolerance at maximal work, with minimal respiratory distress at rest, and says it affects up to 80 percent of athletic horses at some point in their careers. A horse that coughs twice at the start of work and then seems fine is the everyday version of this, and it is not nothing.
  3. 03A contagious respiratory infectioncommonpossible painMerck puts the incubation period of strangles at 3 to 14 days and says the first sign of infection is a fever of 103 to 106 degrees Fahrenheit, with mucoid to mucopurulent nasal discharge, depression and swelling of the glands under the jaw following within 24 to 48 hours. Horses begin shedding bacteria within 2 to 3 days of the fever and continue for 2 to 3 weeks or longer, which is why a coughing horse with a temperature is a biosecurity problem, not just a sick horse.
  4. 04Severe asthma or heavespossiblepossible painMerck describes severe asthma as variable and episodic periods of expiratory difficulty at rest with frequent coughing, plus exercise intolerance, nasal discharge and a heave line from abdominal muscle hypertrophy in chronic cases. The University of Florida puts average onset at 9 to 12 years of age, affecting both sexes equally, with the highest concentration in stabled horses fed hay.
  5. 05Something inhaled, or an irritant in the airpossiblepossible painMerck's overview of equine lung and airway disorders groups causes as direct infection with viruses, bacteria, fungi or parasites, immune-mediated reactions to environmental factors, and inhalation of irritants or toxic substances plus trauma. Ammonia from a bed that is not lifted, arena dust, and smoke all belong in that third group and all are fixable by changing the environment.
  6. 06An upper airway or structural problemless commonpossible painA cough that comes with one-sided nasal discharge, noise at exercise, or difficulty swallowing points upward rather than into the lungs. Merck notes that one-sided or two-sided nasal discharge is a reason for endoscopic examination. This group is found with a scope, not with a guess, and it is the reason a persistent cough with a one-sided discharge deserves a vet.

What to try

  1. 1Take the temperature first, twice a dayA fever separates infection from allergy faster than anything else you can do. Merck gives 103 to 106 degrees Fahrenheit as the fever range that is the first sign of strangles, appearing before the nasal discharge and the swollen glands. Write the readings down. If there is a fever, stop riding, isolate the horse and call the vet before the cough spreads through the yard.
  2. 2Isolate a horse with a fever and a coughMerck's control measures for strangles include isolating new arrivals for 14 to 21 days, physical separation into groups according to infection status, strict biosecurity and separate caretakers for each group where possible, and note that horses shed for 2 to 3 weeks or longer after the fever starts. Shared water troughs, shared tack and a shared groom are how a yard outbreak happens.
  3. 3Change the air before you change the medicineThe University of Florida is direct: the most important treatment for equine asthma is environmental and dietary management to reduce exposure to organic dusts and mold. Its recommendations are keeping affected horses on pasture, avoiding round bales, clean and ventilated spaces, low-dust bedding, and soaking hay before feeding. Merck adds that horses should be maintained at pasture with fresh grass as the source of roughage, because medication cannot resolve signs while allergen exposure continues.
  4. 4Note exactly when the cough happensRecord whether it comes at the start of work and then clears, only when the horse eats hay, only in the stable, only in summer at grass, or all the time. Merck lists summer pasture RAO alongside the stabled forms, so the pattern points at the trigger. A cough that only appears at maximal work with no distress at rest fits the mild to moderate asthma picture.
  5. 5Get the vet to look before you medicateMerck's pharmacological options are corticosteroids for the inflammation and bronchodilators to relieve airway obstruction, which are prescription decisions taken after a diagnosis, not before. A cough with nasal discharge from one nostril, noise at exercise, or trouble swallowing is a reason for endoscopy. Do not work a coughing horse hard while you wait for the appointment.

When to call the vet

  • The horse has a fever. Merck gives 103 to 106 degrees Fahrenheit as the first sign of strangles, before any discharge appears
  • Thick or colored nasal discharge, swollen glands under the jaw, difficulty swallowing, or noisy breathing
  • Any increased effort to breathe at rest, flared nostrils, or a raised breathing rate when the horse is standing still
  • A cough that has lasted more than a few days, or that comes back every time the horse is stabled
  • A heave line along the ribs, weight loss, or loss of appetite alongside the cough
  • More than one horse on the yard is coughing, or a new horse arrived within the last two weeks
  • Coughing with distress, blue or grey gums, or a horse that will not settle. That is an emergency

Not sure it is behavior or pain? How we frame it.

Behavior or pain?

A cough is rarely mistaken for behavior, but what it produces often is. Merck describes mild to moderate equine asthma as nonspecific complaints of poor performance or exercise intolerance at maximal work with little sign of distress at rest, and says it affects up to 80 percent of athletic horses at some point in their careers. That horse does not look sick in the stable. It looks like it has gone lazy, lost its keenness, started backing off in the last minute of a round. The two coughs at the start of every session get filed as clearing its throat. Meanwhile the same horse is working with inflamed lower airways. The other half of the trap runs the other way: an owner treats every cough as dust and never takes a temperature, and a contagious infection moves through the yard while everyone keeps riding. Neither of these is a training question. Take the temperature, note when the cough happens, and fix the air the horse breathes before you decide the horse has an attitude.

Questions people ask

Why does my horse cough at the start of exercise?

A cough in the first minutes of work, with no distress at rest, fits the mild to moderate end of equine asthma. Merck describes that form as nonspecific poor performance or exercise intolerance at maximal work with minimal resting respiratory distress, and says it affects up to 80 percent of athletic horses at some point in their careers. It is worth a vet exam and an honest look at the dust in the hay and bedding, not something to ride through.

How common is equine asthma?

Merck states that around 17 percent of mature horses in northern, temperate regions experience allergen-induced lower airway inflammation, and that mild to moderate asthma affects up to 80 percent of athletic horses at some point during their careers. The University of Florida puts average onset at 9 to 12 years of age, affecting both sexes equally, with the highest concentration in stabled horses fed hay.

When is a coughing horse an emergency?

When there is a fever, when the horse is struggling to breathe at rest, or when the gums look blue or grey. Merck gives 103 to 106 degrees Fahrenheit as the fever that is the first sign of strangles, appearing 24 to 48 hours before the nasal discharge and swollen glands. Take a temperature before you decide it is only dust, and isolate the horse if it is up.

Is my horse's cough contagious?

It can be. Merck puts the incubation period of strangles at 3 to 14 days, says horses begin shedding bacteria within 2 to 3 days of the fever and continue for 2 to 3 weeks or longer, and recommends isolating new arrivals for 14 to 21 days and separating horses into groups by infection status with strict biosecurity. Asthma is not contagious, but you cannot tell the two apart from the cough alone, so treat a coughing horse with a temperature as infectious until the vet says otherwise.

Will soaking hay stop my horse coughing?

It is part of the answer, not all of it. The University of Florida lists soaking hay before feeding alongside keeping affected horses on pasture, avoiding round bales, clean and ventilated spaces and low-dust bedding, and says the most important treatment for equine asthma is environmental and dietary management. Merck adds that medication cannot resolve signs while allergen exposure continues, so the air change comes first and the drugs support it.

What is a heave line on a horse?

A visible ridge along the lower ribs caused by the abdominal muscles working to push air out. Merck describes it as abdominal muscle hypertrophy in chronic cases of severe asthma, alongside episodic expiratory difficulty at rest, frequent coughing, exercise intolerance and nasal discharge. The University of Florida adds that severely affected horses may also show weight loss, poor appetite and respiratory distress. A heave line means the disease has been going on for a while.

Sources

Every figure on this page traces to one of these. We cite registries, associations, government and veterinary bodies, and published cost surveys - not other blogs.

  1. [1]Asthma in Horses- Merck Veterinary ManualeditorialThat equine asthma is a chronic, allergen-mediated inflammatory disease of the lower airways covering inflammatory airway disease, recurrent airway obstruction and summer pasture RAO, that around 17 percent of mature horses in northern temperate regions have allergen-induced lower airway inflammation and up to 80 percent of athletic horses are affected by mild to moderate asthma at some point in their careers, that severe asthma presents as episodic expiratory difficulty at rest with frequent coughing plus exercise intolerance, nasal discharge and a heave line from abdominal muscle hypertrophy, that mild to moderate asthma presents as nonspecific poor performance or exercise intolerance at maximal work, that respirable dust in hay or bedding is the driver, and that horses should be maintained at pasture because medication alone cannot resolve signs while exposure continues. Corticosteroids and bronchodilators are the pharmacological options.
  2. [2]Understanding Equine Asthma (Heaves), VM142- University of Florida IFAS ExtensiongovThat equine asthma is characterized by airway narrowing, inflammation, mucus production and bronchospasm, the clinical signs (increased respiratory rate, intermittent cough at rest, nasal discharge, exercise intolerance, respiratory difficulty, heave line, and weight loss, anorexia and respiratory distress in severe cases), that average onset is 9 to 12 years of age affecting both sexes equally with the highest concentration in stabled horses fed hay, that mold, organic dust and endotoxin in hay and straw are the most common allergic triggers, and that the most important treatment is environmental and dietary management including pasture turnout, avoiding round bales, ventilation, low-dust bedding and soaking hay.
  3. [3]Strangles in Horses- Merck Veterinary ManualeditorialThat the incubation period of strangles is 3 to 14 days and the first sign of infection is a fever of 103 to 106 degrees Fahrenheit, that mucoid to mucopurulent nasal discharge, depression and submandibular lymphadenopathy follow within 24 to 48 hours, that horses begin shedding bacteria within 2 to 3 days of fever and continue for 2 to 3 weeks or longer, and the control measures of isolating new arrivals for 14 to 21 days, separating groups by infection status, strict biosecurity and separate caretakers.
  4. [4]Introduction to Lung and Airway Disorders of Horses- Merck Veterinary ManualeditorialThat respiratory disease causes group into direct infection with viruses, bacteria, fungi or parasites, immune-mediated reactions to environmental factors, and inhalation of irritants or toxic substances plus trauma, that signs include coughing that may be dry or include mucus or blood, nasal discharge, rapid breathing at rest and labored breathing, that one-sided or two-sided nasal discharge warrants endoscopic examination, and that stress and mixing of animals from several sources should be minimized.

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