Coccidiosis and deep litter method


In the Brooder
Mar 30, 2017
I've read a lot of people on here use the Deep Litter Method of maintaining their coops but in my research on taking good care of chicks and avoiding things like cocci we're told to keep clean bedding. Can you please explain how to do both, using the deep litter method and keeping it clean to avoid health issues with the girls?


Jul 19, 2015
North Central Florida
Usually by the time mine are on the deep litter they are past the age where coccidiosis is a real problem. I do brood outdoors but my brooder areas are just "regular litter" as in they get cleaned out regularly. The hens that raise chicks also stay in those brooder areas although they are free to mingle with the flock during the day, and once they are big enough to go up the ramps and hop over the ledges the moms often take them into the main coops to dig around in the deep litter. I've never had issues from any of this.


Jul 19, 2015
North Central Florida
Oh I will mention that my run is also deep litter in a sense in that I do not scoop it out, I just add more carbon to it as regularly as possible (ie grass clippings, leaves, pine needles, coop clean out material, etc). They are exposed to that by about three days old. Again, no issues.


Mar 17, 2015
SW Ohio
We only do Deep Litter in the run, the coop is too dry. We do Deep Bedding in the coop (pine flakes) with a poopboard that gets cleaned daily.


Crossing the Road
12 Years
Feb 2, 2009
Southeast Louisiana
The issue is not keeping it clean but moisture control. The Cocci bug thrives in wet conditions, that's when you are moist likely to have problems. If you can avoid wet Cocci is usually not a problem.

For the deep litter method to work the litter has to be slightly damp, enough moisture for the bugs and microbes that turn the litter into compost to live and reproduce. It's a bit of a balance, you want it damp enough for the compost bugs but not wet enough for the Cocci bugs. Many people manage that balance, it's a fairly wide range.

Technically I don't use the deep litter method, I keep my coop to dry. So when I empty it out I have to compost it before I can use it. So I empty it out in the late fall and put it on my garden. By the time I'm ready to plant it has broken down.

lazy gardener

Crossing the Road
7 Years
Nov 7, 2012
I think that in a well managed DL, the good organisms outweigh the bad guys, so there's a healthy balance. Also, there have been studies done regarding the benefit to chicks that are raised on deep litter, whether it's the typical composting litter, or shavings that are continually topped off, rather than being removed and replaced. Those studies have shown that subsequent broods of chicks actually benefit from the microbes left behind by the previous clutches. They grow faster, exhibit better feed conversion rates, and the mortality rate is less. The theory is that they have a stronger gut flora, and some of those microbes actually produce B vitamins which enhances their growth.

My take away from all of this is: if doing conventional brooding, keep those shavings dry. If using shavings, I tend to top them off, not change them out unless they get wet. I also get some soil into my chicks during the first 2 weeks after hatch to take advantage of that 2 week window of opportunity provided by the antibodies inherited from their mother.


5 Years
Dec 15, 2014
I had a cocci outbreak during my (failed) attempt at running my birds on sand. The sand became full of pulverized poo and saturated by snowmelt and spring rains. I treated for cocci, switched to deep litter, and haven't had another outbreak. That was over two years ago. The deep litter manages the moisture and keeps the cocci in check.

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