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Because your body isn't acclimated to it yet. All that sloshing around in your stomach is hard to get used to; the more you run long distances, the easier it will be on your stomach. Also, when you run long distances, a lot of the blood that aids in digestion is diverted to your muscles, which is why you shouldn't run for a while after you eat.

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Q: Why do you get diarrhea when you run long distances?
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