12/08/2025
The Mysterious Fever of Unknown Origin
He’s just a little off. It’s hard to say exactly what’s going on. But he’s your horse, and you know him so well you pick up on the slightest little nuances when something is wrong.
So, you check him all over: no signs of injury, no strange bug bites, no drainage coming out of the nose, no diarrhea, no cough. Then you take his temperature.
Sure enough, fever. Something is wrong. But what?
Welcome to the world of fever of unknown origin. For both owners and their treating veterinarians, this condition can be fraught with frustration, confusion, guesswork, and a Sherlock-Holmes-like investigative process with some modern technological flair.
Fortunately, through strong collaborations with laboratories and referral clinics, horses with fevers of unknown origin can often get the diagnoses and targeted treatment they need.
“At first, it’s unknown origin—but we hope to give it an origin, and give that horse a diagnosis,” says Toby Pinn-Woodcock, DVM, Dipl. ACVIM, assistant clinical professor in the Department of Population Medicine and Diagnostic Sciences at Cornell University College of Veterinary Medicine, in Ithaca, New York.
Understanding Fever in Horses
More than ever, horse owners are tracking their horses’ body temperatures, our sources say.
Technology has certainly played a role in that—thanks to rubbery digital thermometers that beep with a digital reading less than 30 seconds after being inserted in the horse’s re**um. Veterinarians can also now implant microchips with temperature sensors into a horse’s neck, which send real-time data to mobile phones and alert you if the temperature is abnormal.
When such technology meets the hands of highly observant owners, fevers get noticed right away. “Horse owners are so astute,” Pinn-Woodcock says. “They catch things so early—sometimes before there are other signs.”
Re**al or chip-based temperature readings above 101.5 degrees Farenheit (38.5 degrees Celsius) generally indicate a fever in horses. Unless extenuating circumstances exist—such as excessively high outdoor temperatures or significant muscular effort akin to race training—that means there’s some sort of inflammation in the body, says Julia Felippe, MedVet, MS, PhD, Dipl. ACVIM, professor and immunologist in the section of Large Animal Medicine, also at Cornell.
Fever and inflammation function as the body’s first-line defense mechanisms in response to a wide range of health challenges, she says. Specialized molecules induce fever to help immune cells move and function better, while also creating an unfavorable environment for pathogens (disease-causing organisms) to survive.
Indeed, sometimes owners catch fevers before other clinical signs develop, such as nasal discharge, coughing, or diarrhea. Those additional signs often help pinpoint the fever’s cause within a few days, our sources say. But not all horses develop additional signs, even in the case of infectious diseases.
If an acute fever goes away on its own and stays away, it’s still useful to find out its cause—not only to keep the horse’s medical history current and accurate but also determine whether the fever stems from a contagious disease.
But if fevers persist, or come and go, without any clear reason, Pinn-Woodcock recommends finding out what’s behind them, because they can indicate life-threatening diseases.
First Things First: Biosecurity at the Farm
Until you can prove otherwise, assume any fever of unknown origin might stem from a pathogen that could spread to other horses. That means you need to ramp up biosecurity immediately.
Your feverish horse should go in an isolated stall or paddock where he has no contact and shares neither air space nor water sources with other horses, our sources say. “The next step is to contact your veterinarian for evaluation and advice,” says Felippe. If you get a diagnosis for an infectious disease, you’ll need to follow the biosecurity guidelines specific for that disease to prevent or stop an outbreak.
Keep the horse in isolation while you work with your veterinarian to rule out contagious causes of equine fever common to your region, Pinn-Woodcock says.
Causes of Fever in Horses
A feverish horse could have a wide range of bacterial or viral infections, such as strangles, equine herpesvirus types 1 and 4 (EHV-1 and EHV-4), the tickborne disease anaplasmosis (caused by Anaplasma phagocytophilum bacteria), and equine coronavirus—which are a few of the common culprits, our sources say. But they could also carry fungal or parasitic infections such as guttural pouch mycosis and piroplasmosis. Noninfectious conditions, including cancer, immune-mediated disease, or an immunodeficiency disorder, could also be to blame.
“It can be quite challenging to find the cause of fever,” Felippe says.
Cornell’s Animal Health Diagnostic Center (AHDC) offers a comprehensive plan for homing in on horses’ fevers of unknown origin in more complex cases, says Pinn-Woodcock. The Cornell AHDC provides a long list of possible causes of equine fever and diagnostic tests that can be tailored to specific circumstances. These include cultures and polymerase chain reaction (PCR) tests on whole blood, nasal swabs, cerebrospinal fluid, peritoneal (abdominal) fluid, urine, and f***s for pathogens such as herpesviruses, West Nile virus, coronavirus, adenovirus, strangles, Salmonella, Lawsonia, Leptospira, and more.
That doesn’t mean people should run all these tests, she says. Rather, the comprehensive plan serves as a “brainstorming tool” for practitioners. “It’s kind of a jumping-off point to select tests a la carte given the context of each case,” she explains.
Clues for Fever: Seasons, Regions, and Travel
The hunt for a fever’s origin starts with certain clues, our sources say.
Seasons, for example, play an important role, notes Pinn-Woodcock. “We tend to see more fevers caused by betacoronavirus in the winter months, as this virus survives best in cool, moist environments, and we tend to see respiratory viruses in the early spring, which may be due to increased horse travel during this time of year,” she says.
Region also plays an important role, she explains, especially regarding vector-borne diseases. Vectors are disease transmitters—think ticks and midges. Different regions of the world have different vectors. In the northeastern U.S., for example, equine granulocytic anaplasmosis commonly causes fever in horses—especially in the fall when the ticks carrying A. phagocytophilumbacteria are more prone to bite large mammals. And Potomac horse fever, caused by the Neorickettsia risticiibacteria harbored by aquatic insects such as mayflies and caddisflies, occurs most often in summer to early fall in horses living in proximity to a lake, pond, or river in some regions of the U.S. and Canada. Eastern equine encephalitis (EEE) can cause fever in southeastern and Gulf coast states year-round and in northeastern states during summer and early fall when mosquitoes are present.
Make sure you also consider the horse’s recent travel history, says Pinn-Woodcock. Horses attending shows or other events involving multiple horses from different origins can contract a wide variety of pathogens such as respiratory viruses, she says. Plus, researchers have recently confirmed horses in transit often have slightly weakened immune systems, making them more susceptible to such pathogens.
The travel history of the horse’s stablemates should be considered as well, she adds. Horses that have recently arrived on the premises or have been out traveling and returned home could have brought pathogens with them—without appearing sick themselves. “There’s a lot that goes into these risk analyses,” Pinn-Woodcock says.
The Veterinarian’s Workup on Fever
Workups for fevers of unknown origin start with a detailed history, followed by a thorough clinical exam of each system in affected horses: respiratory, gastrointestinal, musculoskeletal, urogenital, and so on, Felippe says. “You use a multidirectional approach to narrow it down,” she says.
Based on the observations, vets collect diagnostic specimens such as nasal swabs, blood samples, and possibly peritoneal or cerebrospinal fluid for laboratory analyses. They might also analyze the f***s for equine coronavirus or infectious bacteria such as Salmonellaor Clostridium, which cause intestinal disease.
Our sources say that while these samples can be used for specific disease testing based on the case context, complete blood counts (CBCs) and complete serum chemistry profiles can also provide clues. These comprehensive exams can point to trends and even specific organ systems that might be affected, based on values that are within normal range or not. For example, high levels of the enzymes aspartate transaminase (AST) and gamma-glutamyl transferase (GGT) suggest a liver problem, and elevated blood urea nitrogen (BUN) and creatinine point to kidney issues.
“This can be a great place to detect a hint about what’s going on,” Pinn-Woodcock says.
Finally, additional tests might include imaging such as X ray or ultrasound, checking for evidence of inflammation or infection in various internal organs.
Even so, test results themselves don’t necessarily give a definitive answer, says Felippe. Tests might return negative results if the active pathogen shedding and replication period has passed, for example. Positives could represent remnants from previous infection or exposure that aren’t the cause of the current fever, or they could be an inflammatory response to vaccination.
“The veterinarian really has to understand what the results mean and how valid they are,” she says. “Even a positive result needs to be interpreted within the case context.”
On the opposite end of the spectrum, test results might not show anything at all—at least, not initially. “Fevers of unknown origin can sometimes take multiple rounds of testing,” Pinn-Woodcock says. “It’s a process. It can take time for the veterinarian to get to the bottom of it—and patience on everyone’s part. It’s not always straightforward.”
Dedicated Fever-of-Unknown-Origin Test Panels
Within a year of arriving at Cornell’s laboratory, Pinn-Woodcock realized her team was getting lots of calls from equine practitioners seeking help for diagnosing horses with fevers without other clinical signs. “It was confusing for them to figure out what sample types they needed and which tests to request,” she recalls.
So, in 2019 she developed a dedicated fever-of-unknown-origin test panel targeting the most common causes—at least in the northeastern U.S. The panel streamlines the testing process, eliminates confusion, and aids efficiency, leading to faster answers and cheaper costs, she says. The Cornell panel provides results on 10 pathogens within three days. This makes it easier for veterinarians to screen their patients for all these things to help them figure out a treatment plan, Pinn-Woodcock says.
University of California Davis researchers have also developed a fever-of-unknown-origin panel adapted to the western U.S., she adds. Regardless of where veterinarians are, they can ship samples to these labs or use existing panels as models to create their own lists of tests to order from local diagnostic labs.
Still, these dedicated panels don’t cover everything, Pinn-Woodcock adds. They just make it easy to rule out the most common infectious causes. “There are many other causes of fever,” she says.
Recurrent Fevers and Immune Disorders in Horses
Horses affected by fevers that just never seem to go away, or keep coming back after treatment, might have an immune disorder, Felippe says. In her research she’s shown these disorders can be particularly difficult to diagnose due to the immune system’s various cell types and functions, she says. “You could have something that affects one area of the immune system but not the other areas,” she explains. “And we do not have tests for all areas of the immune system, so we can miss the real cause.”
Still, some tests can be “quite revealing,” she adds. Low concentrations of immunoglobulins M and G (IgM and IgG) in a horse’s blood, for example, indicate impaired antibody production. “These horses have a decreased capacity to produce enough antibodies to fight against diseases, making them highly susceptible to various pathogens all the time,” she explains.
The immune system can also overreact, creating exaggerated immune responses, Felippe says. Such immune hypersensitivity leads to frequent fevers and tissue inflammation. “It’s a bit antagonistic,” she says. “The immune system is to use its cells and mediators for protection, while losing control of itself and causing damage.”
Take-Home Message
Fevers flag a health problem, but without other clinical signs it can be tricky to determine what that problem is. Using clues such as season, region, and recent travel history can help narrow down the possibilities, and certain diagnostic labs offer dedicated test panels that can help veterinarians efficiently diagnose—or rule out—the most common causes. Our sources indicate that with hundreds of infectious and noninfectious causes for fevers, identifying the issue often demands time and patience. Diligent, collaborative work among horse owners, vets, and laboratories frequently leads to proper diagnoses and targeted treatment.
The Horse