How to Disinfect Your Farm

You know cleaning and disinfecting exposed surfaces helps prevent disease spread, but what’s the best way to do it?

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How to Disinfect Your Farm
Cleaning and disinfecting a barn and its equipment requires good old-fashioned elbow grease, along with the disinfectant that works best for your situation. | Photo: iStock

Sure, you know cleaning and disinfecting exposed surfaces helps prevent disease spread, but what’s the best way to do it?

You take great pride in your farm, making every effort to keep barns and turnout areas clean, tidy, and in good repair. You and your farm employees follow best biosecurity practices, and your collective work has paid off: Your horses are (knock on wood) free of infection or illness. Yet you know that even with the best of care, pathogens have the potential to slip through.

Think about the horse that hauled in last week for a quick afternoon ride. His owner brought her own buckets, but could he have wiped his nose (Wasn’t it a little runny?) on surfaces your own horses will touch? Or the horse that just moved onto the farm from across the state—could she have brought a communicable disease to the premises with her?

In cases such as these, you’ll want to take extra precautions to limit your herd’s infection risk. This includes thoroughly cleaning and disinfecting particular structures, areas, and equipment on the farm.

Where to Start?

If you think about it, barns are natural reservoirs for infectious organisms. Inside, horses, people, and equipment intersect on a daily basis, and all are important vectors capable of spreading pathogens among horses (and, in some cases, people!). This is why it’s important not to simply focus on disinfecting surfaces in barns and barn areas (walls, doors, paddocks, fences, and gates) to curb disease spread; be sure to address hand tools and other farm equipment, vehicles, and trailers, too.

Cleaning and disinfecting a barn and its equipment can be challenging, in large part because layers of soil, dirt, dust, and organic matter coat nearly all surfaces, which can at the same time contain infectious matter and form a barrier against disinfectants.

Brandy Burgess, DVM, MSc, PhD, Dipl. ACVIM, ACVPM, assistant professor of epidemiology and infection control at the Virginia-Maryland College of Veterinary Medicine, in Blacksburg, stresses that disinfection is a multistep process that involves removing visible debris, scrubbing with a detergent, rinsing, and then applying a disinfectant. Because disinfectants work best on “pre-cleaned” surfaces, it is essential that you remove as much visible organic debris as possible.

“Detergents contain surfactants, which aid in the dispersal and removal of organic material on surfaces,” Burgess explains. “A detergent allows the disinfectant to reach microorganisms; it does not reduce the contact time necessary for disinfection, which as a chemical reaction takes time.”

How to Disinfect Your Farm
High-pressure washing can be particularly helpful for cleaning porous surfaces; however, the force of high pressure water may aerosolize microorganisms and contaminants, which contributes to further environmental contamination. | Photo: Anne M. Eberhardt/The Horse

Elbow Grease and Cleaning

Some good old-fashioned scrubbing and rinsing can remove the majority of microorganisms from barn surfaces. “Applying a disinfectant adds another level of confidence for lowering the burden of microorganisms to relatively inconsequential levels,” says Burgess.

Before you get started, relocate horses from the area you’re about to clean and disinfect. You might also need to remove all bedding and the top layer (6 to 12 inches) of stall surface dirt to clean and disinfect stalls adequately. Basically, this cleaning requires a lot of elbow grease–scraping, brushing, and scrubbing away organic debris splattered on walls and floors.

For the initial cleaning, start from the back of the barn and work your way forward, trying not to retrace your steps. Start at the top of walls and work down, directing wash and rinse water toward drains. Scrub all firm surfaces and/or use a low-pressure (less than 120 psi) power washer. Many barns have hard surface floors but in the case of dirt, remove the top layer as best as possible.

“Power washing can be useful both at low pressure (90-120 psi) and high pressure (>200 psi),” says Burgess. “High-pressure washing can be particularly helpful for cleaning porous surfaces; however, the force of high pressure water may aerosolize microorganisms and contaminants, which contributes to further environmental contamination.” This is something to keep in mind if you are trying to disinfect afer housing a sick horse or following a disease outbreak.

She also points out that hard water might reduce some disinfectants’ effectiveness. And well water can contribute to recontamination, so be sure to test it for microbial contamination before using it for cleansing and rinsing. If it comes back positive for significant pathogenic microbes, consider alternative sources for the horses’ drinking water, including having clean water delivered.

Pay careful attention to organic debris in corners and other tight spaces. “It is not possible to effectively clean and disinfect cracks, seams, or porous surfaces (such as wood and concrete),” says Burgess. “Facility managers should seal these areas (e.g., with polyurethane or marine varnish) and/or replace porous materials with nonporous surfaces to facilitate effective disinfection.” Nonporous surfaces include stainless steel, glass, and sealed ceramic materials.

With respect to corners, Burgess recommends rigorous regular cleaning with detergents to prevent bacteria from forming their persistent, self-preserving “biofilms” on moist surfaces. “Scrubbing and (careful) rinsing are the most important parts of the process, removing up to 90% of microorganisms as well as decreasing biofilm formation,” she says. This washes away debris and detergents, sending them into the drain system.

Once you are confident that you have cleaned and rinsed all surfaces thoroughly, allow them to air dry, or remove excess water from walls and floors with a squeegee. Opening windows and doors in the barn also helps hasten drying.

Time to Kill Those Bugs

After surfaces are dry, you can move on to the disinfection stage. While thorough cleaning might eliminate all but 10% of bacteria, disinfectants attack 6-7% of the bacteria and viruses that remain. The only way to remove all pathogens is sterilization, which is not applicable to a farm environment.

Before disinfecting, don your protective clothing, eye protection, and respiratory mask; then saturate all surfaces with the selected germicide. Apply disinfectant at the manufacturer’s specified concentration; extra water dilutes it further and reduces its efficacy.

“Directed misting application of a disinfectant is useful for disinfecting areas that can’t be directly cleaned with water, such as overhead lighting and electrical conduits,” Burgess explains. “Facility owners should seek professional assistance with this type of disinfectant application and ensure that appropriate personal protective equipment is being used.”

Remember to clean and disinfect equipment in the stalls and barn, as well. This includes waterers, mangers, feed buckets, blanket racks, horse toys, and cleaning equipment, such as rakes, shovels, and wheelbarrows, among other items horses might touch in your barn. Prior to cleaning and disinfecting the barn, remove all these items so they don’t get in the way and so no surface is missed. You can clean and disinfect the tools separately, rinse them thoroughly, and then place them in the sun to dry (ultraviolet light also has germicidal effects). Don’t forget to clean and disinfect tractors, horse trailers, tires, mats, mud guards, and trailer ramps, as these can also harbor microorganisms.

The longer disinfectant contacts a surface, the better. “Contact times vary with the disinfectant, concentrations, and environmental conditions,” says Burgess. “Consumers should check the manufacturers’ labels. While a general guideline is 10-15 minutes, it could take longer in colder ambient temperatures.”

Drying usually takes about half an hour or less in a dry climate and/or if you use fans. Once dry, you might want to apply another layer of disinfectant, especially if you’re attempting to control an infectious disease outbreak.

Difficult-to-Disinfect Areas

Scott Weese, DVM, DVSc, Dipl ACVIM, professor at the University of Guelph in Ontario, Canada, has a special interest in infection control. “Good infection control and biosecurity practices should reduce the risk of an infectious horse being turned out into a paddock or pasture, thereby reducing the concern for disinfection methods” for these enclosures, he says. But, when a circumstance arises that requires diligent disinfection throughout the farm, what can you do?

Regarding the feasibility of disinfecting paddocks and fences, Weese says, “It is hard to disinfect rough and porous surfaces, such as wooden fence rails, and the amount of fencing that would have to be disinfected is often prohibitive. Sunlight is a good disinfectant for these areas, killing most pathogens fairly quickly, especially if it’s dry.

“However, the risks of paddocks and fencing as reservoirs for infection are probably limited for most pathogens,” he continues. “It is most important to pay attention to horse-to-horse contact as well as common fomites (inanimate objects that transfer pathogens) and vectors such as tack, peoples’ hands, and clothing.”

Don’t forget to disinfect water tanks and vessels; water is a known vehicle for transmitting many diseases, including strangles (caused by Streptococcus equi). “Drain the tanks, scrub to remove debris, apply a disinfectant for the required contact time, and then rinse thoroughly to remove any disinfectant residue,” says Weese. The same procedure applies to feeders, especially those shared among horses.

Types of Disinfectants

Germicidal activity (the ability to kill microorganisms) depends on chemical concentration, temperature, pH level, and the presence of organic debris. There is no single disinfectant that possesses all desirable characteristics: the ability to kill all pathogens; nontoxic to horse and human; environmentally safe and biodegradable; noncorrosive and not harmful to surfaces; and stable and effective at wide temperature ranges. Often, property owners must compromise on some of these features, depending on what’s most important for their situation. Always read the label on the back of the disinfectant bottle to identify the names of active ingredients so you know what you are using and how to use it.

“The key for success is in using the disinfectant correctly,” Weese advises. “The best disinfectant won’t work if used improperly.”

Peroxygen compounds

Accelerated hydrogen peroxide (AHP) is Weese’s preferred disinfectant. “While it is more commonly used in clinics than farms, some are starting to use it as a general purpose disinfectant,” he says.

The disinfectant is comprised of hydrogen peroxide, surfactants and wetting agents to maximize penetration, and chelating agents to reduce water hardness. A cleaning agent as well as a disinfectant, AHP is relatively safe to use and doesn’t persist in the environment. You can use it on most surfaces, although it might cause discoloration or pitting on copper, brass, or nonferrous metals.

Virkon S is another broad-spectrum germicidal peroxygen compound that’s effective against equine viruses and bacteria. Weese says it’s somewhat more caustic than AHP but quite effective.


Bleach can be an effective disinfectant for surfaces that have been cleaned to remove all organic matter, which would otherwise inactivate the chlorine as a germ-killing agent (this can make it unsuitable as a primary disinfectant on the farm). Bleach is readily available, very inexpensive, and extremely effective as a broad-spectrum germicidal chemical, targeting Gram-negative (e.g., Salmonella) and Gram-positive (e.g., S. equi) bacteria as well as spore-forming bacteria (Clostridium, also spore-forming) and some viruses.

Always read the label instructions, but a general rule is to mix ¼ cup of household bleach in 1 gallon of water. Never use chlorine in an undiluted form, and never mix it with other chemicals because it can form toxic gases. Always wear protective eye and respiratory gear. Be careful using bleach on metal, plastic, or some fabrics, as chlorine can damage those materials.

Quaternary ammonium compounds

In this chemical class we have ammonium chloride. It’s ineffective in the presence of organic matter, so again, pre-clean surfaces thoroughly. On the plus side, it’s not as toxic as some of the other compounds and poses minimal risk of causing irritation. Couple it with an appropriate detergent (i.e., one with a neutral pH, such as Joy or Ivory soap).


Phenolic disinfectants kill viruses, bacteria, and fungi and are effective even in the presence of organic debris. However, says Burgess, they are carcinogenic (have the potential to cause cancer) and environmentally unfriendly. In addition, phenols are highly corrosive to metal, extremely toxic and potentially fatal to cats, and cannot be used with cationic (positively charged ion, such as some dish or hand-washing soaps) or nonionic detergents, because their interaction renders them ineffective.


While formaldehyde and glutaraldehyde are very efficacious, even in the presence of organic matter, our sources do not recommend using them for farm disinfection due to their toxicity and carcinogenicity.


Chlorhexidine is an example of this disinfectant class. Its germicidal activity is quite effective in the right conditions. Because it works within a specific pH, it cannot be used with anionic detergents, and organic matter inactivates its disinfectant capabilities.


Povidone iodine used at a 10% concentration is efficacious as a disinfectant against both viruses and bacteria. It is useful for hand-washing and equipment-cleaning, but probably isn’t appropriate for disinfecting an entire barn—it could be cost-prohibitive and will stain some surfaces.


Ethyl or isopropyl alcohol can inactivate some bacteria, fungi, and viruses. However, organic debris renders alcohols ineffective, and alcohol is flammable—a safety risk on farms.

Detergent disinfectants

These are intended for use in a one-step process. While the detergent contains surfactants to help break up organic matter, a sanitizer reduces the amount of microbial contamination on inanimate surfaces to a level considered “safe.” However, Burgess says these are not particularly effective in equine environments coated with organic debris.

Take-Home Message

“It is important to recognize that cleaning and disinfection is a multistep process,” says Burgess, adding that the appropriate disinfectant for a situation depends on the microorganism of concern and the environment. She strongly recommends that users adhere to manufacturers’ label directions and says,   “Horse owners should confer with their veterinarian to determine an appropriate cleaning and disinfection plan for their unique facility and situation.”


Written by:

Nancy S. Loving, DVM, owns Loving Equine Clinic in Boulder, Colorado, and has a special interest in managing the care of sport horses. Her book, All Horse Systems Go, is a comprehensive veterinary care and conditioning resource in full color that covers all facets of horse care. She has also authored the books Go the Distance as a resource for endurance horse owners, Conformation and Performance, and First Aid for Horse and Rider in addition to many veterinary articles for both horse owner and professional audiences.

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