my chickens poop in their nesting boxes

yes i think they are sleeping in them and im pretty sure their nesting boxes higher then their roost
 
That is the problem then, they are naturally going to sleep on the highest thing they can get their feet on. Your nesting boxes need to be lower than your roost(s) and that should solve your problem.
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I'd add also that whenever you do catch them sleeping in the boxes, pull them out. It's a bad habit that you want to discourage. Especially when you have pullets not laying yet, they don't have any sense of the purpose for the boxes and will try to sleep there. If my whole flock is pullets I just wall off the boxes until it is time for them to begin laying so they don't establish that bad habit. Chickens are trainable to a certain extent! When I close up and count heads at night I check to see that everyone is on the roosts where they belong.

I have another theory about pooping in nest boxes. I'd be interested to hear from anyone what they think of it. I believe that if you have too many boxes for the size of your flock, there is not enough competition and demand for them. In that situation low-ranking hens might just hang out in a box all the time in order to avoid social interaction. I have three boxes for 16 hens and while most books on keeping chickens would probably say you needed many more for that size flock I find it works fine.
 
I guess they work it out... take turns? They are kind of large boxes so sometimes I'll find two in a box together. I'm not saying 3 boxes for 16 hens is an ideal ratio, just perhaps the low end of the workable range. It isn't what I designed my coop to be, I began with 6 hens....

What got me thinking about this was housesitting for a friend, who has probably 14 boxes for about 20 hens. I've never seen such gross eggs as I take from that coop. Every single one is completely smeared with manure. Whereas my eggs come in the house so clean I rarely have to wash one. Of course there could be other reasons for this difference, but I did notice in that coop there are several low-ranked hens that are always in the nests though they aren't broody.

How would I know if the hens were really having trouble with too few boxes? I've been going with the assumption that I'd find eggs laid in corners, on the floor, wherever. But I don't.
 

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