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It could be to see if they will come into heat or are pregnant.

That, or, if they are positive for any contagious disease they might have or are carriers for that can be transferred to other horses.

Answer 2:

It should be noted that it's not just mares that are put into a two week quarantine. Two weeks is the standard minimum for any horse in quarantine.

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Q: Why are mare horses put into quaratine for two weeks?
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