Emergencies/Illness Predators & Pests

Disinfecting For Chicken Pathogens

In the summer of 2020 I got together with Dr Vicki Bowes, avian vet/pathologist to look at a number of chicken health cases I had collected for her diagnosis. Since that time we have gotten together every few months to chat about other cases as a learning experience for both me and my readers, which I turned into the series Avian Pathology Cases.

It’s been interesting to learn about survival times of various pathogens and what we, as chicken keepers, can do to try and eradicate them, if possible. Some are relatively easy to deal with, while others live in the environment for months, if not, years.

I scoop poop as often as I can, season permitting: daily in the summer when it’s light and a couple of times a week over the dark winter. Once or, if I am ambitious, twice a year I do a deep clean which takes about five or six hours, spread over two days.

Decontaminating your coop is essential in the prevention of viral and bacterial infections, coccidia, internal worms and external parasites. For some, the control of Salmonella, is important, especially in laying hens. It 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.

In order to reduce Salmonella and other health risks, a complete dry cleaning, washing and disinfection of your coop at least once a year is recommended. It may seem like a lot of work, but it’s important not to skip any steps and to complete them in order.  I recommend that you chose a sunny day, which will speed up the drying times between steps.

My coop has a full concrete foundation including the bottom one foot of the perimeter walls and has three pop doors that I can open to shovel, sweep and hose the contents outside. The interior walls are plywood and can withstand pressure washing. Depending on the size and materials of your coop (including having a dirt floor) you may have a more difficult time cleaning and disinfecting it. Do what you can to the best of your ability.

Dry Cleaning

  • Wear a mask and gloves
  • Start by emptying your coop of all your birds and equipment (feeders, waterers, storage bins, shovels, etc).  
  • Sweep or use a leaf blower to remove dust and dirt off every surface and fixture.
  • Remove all bedding from the floor and nest boxes.


  • Use warm/hot water if possible. I use a garden hose with cold water, as that is what is available.
  • Soak the heavily soiled areas (perches and roosting areas, floors, etc.) thoroughly so that dried poop softens.
  • Scrape poop from roost bars and floors.


  • Using dish detergent wash every surface, especially areas where dirt accumulates.
  • Make sure hidden areas are thoroughly cleaned.
  • Sweep out puddles, as they can become breeding grounds for Salmonella.
  • Remove all food and water from containers and then clean them.


  • Open all windows, doors and vents and air-dry your coop and equipment.


  • Inspect your coop and see if there are any holes or damage and seal them to avoid intrusion by rodents or predators like mink.

Disinfection  (Don’t skip this step)

  • Disinfectants should be applied only after the coop and equipment have been thoroughly cleaned, ideally right after washing.
  • They can be applied by using a spray, aerosol or fumigation.
  • White vinegar (acetic acid) can kill some bacteria and viruses but many commercial disinfectants are more effective.
  • Recommended products include Virkon, Pinesol or generic bleach. Follow the manufacturer’s directions for mixing and dilution of these disinfectants; usually it’s 1:10.
  • Apply at the rate of one gallon of diluted disinfectant per 150-200 square feet of surface area.
  • Soak waterers and feeders in 1 tablespoon bleach per gallon of hot water.
  • Allow everything to dry before returning equipment, adding fresh bedding or refilling feeders and waterers.

If you have had an outbreak of illness then use the strongest disinfectants possible, that are also safe for your flock.

This guide will give you some idea of how long various pathogens can survive in the environment without a host.

Pathogen Survival Time In The Environment (Outside of Host)

3-4 weeks at 22C/72F or 4 months at 7C/45F

Avian Tuberculosis

10 years

1 year

Fowl Cholera  

3-4 weeks

4-6 months

1-2 weeks at 22C/72F or 4 months at 7C/45F

1-2 weeks at 22C/72F or 4 months at 7C/45F

2-4 years

1-3 days at 22C/72F or 3-4 weeks at 7C/45F

1-3 days at 22C/72F or 3-4 weeks at 7C/45F

Newcastle Disease

4-6 months

3-4 weeks at 22C/72F or 5 months at 7C/45F

Trichomonosis (Canker)

1 week at 22C/72F or 3-4 weeks at 7C/45F

Credits: Dr Vicki Bowes, DVM; All About Chicken Diseases & Respiratory Symptoms; Dr Michael Darre, University of Connecticut. Featured image credit: Biocamp

0 comments on “Disinfecting For Chicken Pathogens

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )

Connecting to %s

This site uses Akismet to reduce spam. Learn how your comment data is processed.

Bitchin' Chickens

Everything You Need To Know About Small Flock Chickens & More

%d bloggers like this: