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I think I've had this problem before. After a car gets to be a few years old and you run the fan, it stinks, and that's not even with the re-circ on. What's the deal? Is there some way to kill whatever's smelling things up? Is there some filter that needs to be cleaned?

 
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Cabin filter gets replaced around 25k. I would start there.

Get a good flashlight and look around the duct work while it is removed for visitor clues.

 
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Thanks, I'll look at it.