The most common cause of this is a lack of clean bedding. This doesn't mean that you have to remove all the bedding and clean the cage every day, but you should remove any wet bedding--be it wet from urine or water--as well as that containing any stool. However, if it's been a while since you did a thorough cleaning job, I'd do that first then vow to stay on top of the problem daily. Not only will your rats smell better, they'll also be healthier and happier, too.
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