The basic method for cleaning and disinfecting stalls and trailers is similar to the way you clean smaller tools. "First, remove all organic matter, including hay, manure and bedding as well as buckets and removable objects, and then scrub all surfaces with detergent and water; then rinse," says Roberta M. Dwyer, DVM, of the University of Kentucky. Always start at the top and work your way down toward the floor so that all of the dirt will flow down away from the areas you've just cleaned.
"Avoid using high-pressure washers, which can aerosolize some pathogens [making them airborne], where they can rest on rafters, ledges or other horizontal surfaces," says Dwyer. "Once they land there, dust can then mix with the dried aerosols and be blown down into horse areas."
Ask your veterinarian to recommend the most appropriate disinfectant for your situation. Bleach is not the best choice for porous materials, such as wood, but there are products made specifically for use in large-animal stalls or trailers. "Be wary of disinfectants that are corrosive to metal, and be cognizant of any exposed wiring when using water," says Dwyer.
Read and follow the manufacturer's directions carefully. Typically, you would spray the solution onto the walls, again going from top to bottom, and allow it to dry. Also make note of any safety precautions described on the label. You'll want to dress in long sleeves and pants to protect against splashing chemicals on your skin. "Always use protective clothing, including gloves and eye protection," says Dwyer.
Stalls with porous surfaces—including unfinished wood and dirt floors—cannot be completely disinfected. Sealing stall walls with varnish will make them less porous and easier to clean. To clean dirt floors, remove as much manure as possible, and allow the surface to air-dry thoroughly before adding bedding. For added cleanliness, lay down some type of stall mats, which can be sanitized more efficiently.