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Cleaning and Disinfecting Your Poultry House

As spring approaches, the time is almost here to do a good cleaning and disinfecting of your poultry facilities after the long winter. This is especially true if you are considering bringing in new birds or replacing your flock, be they layers, meat birds or show birds. Decontaminating your poultry house is crucial in order to prevent Marek’s disease, mycoplasma, respiratory viruses, E.coli, mites, and other poultry health problems. Even more important is the control of Salmonella Enteritidis (SE), especially in laying hens. SE can colonize in a chicken’s intestinal tract without necessarily causing obvious disease in the chicken itself. This may lead to the organism invading other tissues and eventually finding its way into the reproductive tract and ovary, contaminating the egg itself.

Young chickens in a wood and wire coop. Photos by New Entry Sustainable Farming Project

Young chickens in a wood and wire coop. Photos by New Entry Sustainable Farming Project

In order to reduce SE and other health risks, a complete dry cleaning, washing and disinfection of the poultry house after each flock or at minimum once each year is recommended. Successful cleaning is hard work and requires systematic completion of several sequential steps. Every step is important. Skipping one step or doing an incomplete job at any point will make the next step harder and lead to failure.
Start by removing all birds from the building to be cleaned, along with all equipment that can be cleaned in another place, such as feeders and waterers.

Dry Cleaning
Sweep or blow dust and other loose dirt off ceilings, light fixtures, walls, cages or nest boxes, fans, air inlets etc. onto the floor. Remove all feed from feeders. Scrape manure and accumulated dust and dirt from perches and roosts. Remove all litter from the floor.  Litter can be added to a compost pile. Sweep the floor to remove as much dry material as possible. With a small coop, a wet-dry shop vacuum does a good job of removing this material. However, be careful to clean the filter often as the fine dust from the coop may easily clog the filter and make the vacuum work harder or lead to burn out of the motor.

Wet Cleaning
Turn the power off to the building prior to using any water for cleaning. Wet cleaning is done in three steps: soaking, washing and rinsing. Warm or hot water will do a better job getting through organic matter than cold water. You can use a cheap neutral detergent, like dish soap.

Soak the heavily soiled areas (perches and roosting areas, floors, etc.) thoroughly. Use a low pressure sprayer to totally soak all surfaces. Soak until the accumulated dirt and manure has softened to the point it is easily removed.

Wash every surface in the building, especially window sills, ceiling trusses, wall sills and any surface where dirt and dust may accumulate. The washing solution can be either a neutral detergent (ph between 6 and 8) or an alkaline detergent (ph above 8). Alkaline substances vary in their strength with the strongest causing burns and internal injuries if swallowed. A mild alkali is baking soda (sodium bicarbonate) and moderate alkalis include household ammonia, borax and trisodium phosphate. Strong alkalis include washing soda (sodium carbonate) and lye (caustic soda). Mix in hot water—160oF or hotter is best.

Maintaining a clean, dry environment is especially important for young chicks.

Maintaining a clean, dry environment is especially important for young chicks.

A high pressure sprayer is good for this step, but manual scrubbing with a moderately stiff brush is one of the best ways to insure a thorough cleaning. Inspect manually to be sure you have removed all of the dirt and manure from all surfaces. Make sure you carefully clean electrical parts.  You may have to remove cover plates and vacuum those areas.

If you have metal surfaces with hard water scale, then you will need to use an acid detergent on those surfaces to remove the scale. Acid detergent involves acid as the major component which is used in dissolving mineral deposits (Calcium and Magnesium precipitates) or hard water deposits from equipment surfaces. Two main groups of acid detergents are: inorganic (HCL, H2SO4), and organic (Vinegar, Citric Acid).

A final rinse immediately after washing is recommended to remove any harmful residues and to obtain a spotless building. Mop up puddles as they can rapidly become breeding grounds for salmonellae.

Thoroughly air-dry the building if disinfection cannot immediately follow rinsing. Open all windows and ventilation openings. Use a blower or fan if available. Cleaning on a dry, sunny day helps in the drying process.

Make any repairs to the structure prior to the final disinfection step. Seal any rodent entry holes at the outside and inside of the building. Apply a small amount of spray foam insulation into the hole, then pack in fine steel wool and top with more spray foam.


This is a crucial step which the small flock owner might normally overlook. Disinfectants should be applied only after the building and equipment have been thoroughly cleaned, ideally right after rinsing. Disinfectants can be applied by sprays, aerosols or fumigation. Don’t be intimidated by the thought of “fumigating” your hen house: for most small flock facilities, using a garden type sprayer is the easiest method, and chances are you already have a suitable disinfectant around the house. The types of disinfectants generally used are phenolic compounds (e.g., Pine-sol, One Stroke, Osyl),  iodine or iodophors, (e.g., Betadine and Weladol), chlorine compounds (e.g., Clorox, generic bleach), quaternary ammonium compound (e.g., Roccal D Plus) and oxidizing compounds (e.g., Virkon S, Oxy-Sept 333).

Follow the manufacturer’s directions for mixing and dilution of these disinfectants.  A good rule of thumb is to apply at the rate of one gallon of diluted disinfectant per 150-200 square feet of surface area. For a more thorough disinfecting, soak waterers and feeders in a 200 ppm chlorine solution (1 tablespoon chlorine bleach per gallon of boiling water).

Michael Darre

Dr. Michael J. Darre is Extension Poultry Specialist at University of Connecticut. He can be reached at michael.darre@uconn.edu or (860) 486-1008.


  1. John on May 22, 2014 at 8:38 am

    This is an excellent article, and I admit to missing on some of these steps. Thanks for the step by step process; it’s something I plan to tackle this weekend as selling eggs is a big part of my small farm business.

  2. Gbeinbo Hope on October 16, 2014 at 11:46 am

    please, i did an assistance concerning my project work (assessment of post cleaning salmonella contamination in poultry. please help me if you can with some relevant materials. thanks

  3. Anthony Phillips on October 21, 2014 at 9:00 am

    I work for a Egg Company and we have a 2002 0r 2003 Diamond 8400 Series Egg Grading Machinery and we are have problems cleaning the stainless steel parts which there can be no water applied to the machine because of the electronics. Need tips on how to get the egg shells and dried egg off of the steel stars and the perch that runs in a machine that detect cracked , dirt and blood detectors if you know what i am talking about. Call me at 912-310-0906. Thanks AJP.

    • ann on December 28, 2019 at 6:38 pm


      ACID is the best solution and method to clean the sections such as star wheels and areas of egg protein or egg shell. An alcohol based sanitizing wipe or product is another approved method for no water zones in egg processing.

    • Brad on June 9, 2020 at 4:36 pm

      Remove the JDM plastic borders ,(they’re the black ones on the edges). Pick up the stainless star screen and scrub with a brush and boraxo cleaner. Apply a thin layer of crisco lard and let sit for a day, then come back with boiling water and rinse off.

  4. Jennifer E on February 8, 2015 at 2:08 pm

    We live and work on an 8 house chicken farm with an average of 250,000 chickens every 7-8 weeks. The owners and the company decided they wanted to bleach the houses because the ammonia levels were too high. The fumes from this are leaking into our house and causing myself and my newborn respiratory problems. What alternative to bleach can I suggest to them that will neutralize the ammonia without giving off toxic fumes?

  5. Sarah Diana Nechamen on February 9, 2015 at 12:59 pm

    Hi Jennifer,
    Good question! I’ve sent an email to the author asking him to respond and copied you on the message.

  6. Tonya R on April 9, 2015 at 6:11 pm

    Jennifer E, White Vinegar is a great alternative to bleach

  7. Margaret Brandt on May 8, 2015 at 12:45 pm

    If there has been SE in coop and all birds culled,how long before new birds can come in after thorough cleaning and disinfection? Should we just build another coop?

  8. Sarah Diana Nechamen on May 8, 2015 at 1:41 pm

    Hi Margaret,
    I’ve sent your question over to the author of the article and copied you on the email.

  9. kari on July 24, 2015 at 12:18 am

    Great step by step for cleaning my hen house. But I have just noticed mites on my girls. I am going to dust them all with poultry dust after I thoroughly clean the coop. But Will this process kill the lice and mites that are in the coop? I think I’ll be using bleach for the disinfecting part.

  10. Carli Fraccarolli on July 24, 2015 at 1:02 pm

    Hi Kari,
    I would suggest that you contact the author of this article, Dr. Michael J. Darre. He should be able to answer your questions about poultry lice/mites. His contact information can be found at the end of the text.

  11. Jeanne on August 21, 2015 at 8:40 pm

    What about how to clean the chicken run after having salmonella enteritidis?

  12. Anne Marie on September 18, 2015 at 4:10 pm

    We have 2 chickens in a coop with a sand floor. A small amount of hay is in their above-ground nest box. We keep almost no hay on the property because we are a program that houses 20 disabled raptors (hawks, falcons, etc.). Hay greatly increases the risk of aspergilloses. We scoop daily and keep the rest of the coop very clean but what is the best way to disinfect the sand? Would wood shavings be a safer alternative than hay?

    • zsuzsanna pragai on June 29, 2020 at 5:17 pm

      I always use wood shaving in the egg laying boxes and pine based bedding (aubiose or easichick) on the floor. Hay isn’t recommended for the fungal infection possibility.

  13. Alvin Garfield on March 11, 2016 at 6:42 am

    Very Informative article. I will definitely follow your advice. Keep sharing such informative things.

  14. Barbara Hunter on March 26, 2016 at 8:59 pm

    We bought a new chicken & put her in the hen house with 30 of our other chickens & within 2 weeks all the chickens had CRI & had stopped laying eggs. We had to cull our whole flock. We disinfected the whole coop, inside & out, feeders, waterers, fences, ground, everthing with bleach (1C to 2 gal of water) How long before we can start a flock & put them in that coop?

  15. Zequek Estrada on May 5, 2016 at 8:40 pm

    Michale, this was interesting learning about how to keep a poultry house clean. Washing everything down seems like a process could take a long time. Is this something you would recommend hiring a professional service for?

  16. Terri on July 5, 2016 at 6:24 pm

    I have the same question about how to disinfect a sand floor. In FL. it’s about the only option we have. The chickens do a lot of digging, and quite deep as they’re trying to reach cool spots in the summer. What is the best thing to use on sand where it can’t be dried.

  17. Terri on July 7, 2016 at 10:03 am

    Thank you very much. I hope to hear from him soon. Out of nowhere my flock of 38, with broody hens getting ready to hatch chicks within a weekish, have come down with some sort of respiratory issues. I have put them on antibiotics, vetRX, and the vitamins and probiotics, and they’re getting better but I’m worried about any residual effects and the chicks, especially when it’s impossible to dry sandy soil.
    Thanks again!

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  19. Marnas farm on October 2, 2016 at 1:11 pm

    How do i disinfect a three step poultry pen built with wood

    • Bolanle on February 19, 2021 at 2:07 pm

      This was a good simple to follow step by step article and I have used it immediately to clean and disinfect my pen ready for arrival of a new stock. Thanks.

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  22. virginia woods on October 16, 2017 at 5:03 pm

    i have a sick rooster and hen . and i have put them down. how do i disinfect my coop where the sick chickens are?

    • Tara Hammonds on October 18, 2017 at 2:05 pm

      Hi Virginia,
      It is going to depend on what the chickens were sick with, but as long as you follow the cleaning, washing, nd disinfecting steps listed in the article, you should be fine. You may want to double check with a local vet to be sure.

  23. Mirza Ghafoor on January 19, 2018 at 9:14 am

    Dear Dr Michael
    What is the best dosage of dilution if we disinfect farm with Chlorine tabelts ( Troclosene sodium) ?
    In presence of poultry birds or in vacant shed.

    • Carli Fraccarolli on February 6, 2018 at 1:17 pm

      Hi Mirza, thanks for reaching out to Dr. Darre. As he does not work in the Small Farms Program office, you will have to contact him directly with your question. Please email him at michael.darre@uconn.edu or call (860) 486-1008.

  24. Theophilus on May 13, 2018 at 7:52 am

    If there has been SE in coop and all birds culled,how long before new birds can come in after thorough cleaning and disinfection? Should we just build another coop?

    • Talia Isaacson on May 17, 2018 at 9:34 am

      Hi there,
      I’d recommend getting in touch with the author of this article. He can be reached at michael.darre@uconn.edu or by phone at (860) 486-1008. Hope this helps!

  25. Chienge Nyaroka on December 17, 2018 at 7:28 am

    I would like help with disinfecting my chicken house and grounds following complete removal of a stock that had coryza infection

    • Kelsie Raucher on April 2, 2020 at 12:51 pm

      Hi Chienge,

      The author of this article, Dr. Michael J. Darre, might know more about coryza infection. He can be reached at michael.darre@uconn.edu or (860) 486-1008.

  26. Chienge Nyaroka on December 17, 2018 at 7:35 am

    please advise on disinfection following removal of chickens infected with coryza

    • Kelsie Raucher on March 26, 2020 at 2:50 pm

      Hi Chienge,

      I’d recommend reaching out directly to the author of the article with your question. Michael can be reached at michael.darre@uconn.edu or (860) 486-1008.

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  28. paul on January 5, 2020 at 10:25 pm

    This a nice write on poultry disinfection, this helped me on my assignment.

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  31. amel sm on November 18, 2020 at 6:03 am

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  32. ranithrao on February 11, 2021 at 1:03 am

    Thank you , For Giving information About Poultry Disinfection and also what is Poultry and how to Cleaning..

  33. Paul odwory on March 18, 2021 at 8:37 am

    Thanks. I would also want to invest in this business. I need some advise on poultry farming.

  34. Shammy Peterson on July 1, 2021 at 9:57 pm

    You got my attention when you said that a high-pressure sprayer is good for washing every surface in the building, especially window sills, and wall sills. My father is looking for his barn to be cleaned and disinfected. He said that he does not want his livestock to get sick due to dirt and other issues. I would ask him to shop for disinfectant mats and sprayers.

  35. House Clean Kuwait on August 24, 2021 at 2:09 am

    I want to thanks Cornell Cals for sharing this useful Cleaning guide for poultry farms/houses.

  36. John on September 26, 2021 at 1:49 am

    Very much I’m pleased with step to step guide. thanks and keep on.

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