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This can be difficult, you must 'potty train' the horse. Some horses will not do it no matter what and you'll just have to live with it. However you can try to train them through positive reinforcement, such as clicker training. You'll need to spend several days with the horse. Begin by introducing the clicker to the horse, make the clicking noise and give a treat, this reinforces that the clicker is a good thing. Then when you see the horse begin to go potty either try to move him away from the shed or refuse to give him a treat. When the horse goes outside, click the clicker and give a treat and a pat, do this each time the horse goes to the bathroom outside. It can take days or weeks for it to become reinforced, but it can be done. If this does not work, then try spreading the horses hay around the shed, as most horses will not poop where they eat, if he poops on his hay, then he likely will not care nor pay attention to any type of potty training.

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Q: How do you stop a horse from pooping in run in shed when he has the whole pasture?
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