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Motherboards come equipped with fans now?! I've been working with too old hardware, I'm just used to seeing those funky heatsink units...
It's possible that the fan is broken, but it's still possible that it's something else. Do you know if your system supports "smart" cooling modes? If it does, it could just be smart control. Smart control will basically only turn the fan on when the temperature reaches a defined limit. I use this with my processor to reduce noise; the fan only kicks in when the processor's temperature starts to rise above, say, 37 deg C (I'm using a Sempron, they run nice and cool). It's possible that the thermal sensor died, if that's the case.
Fans are generally cheap to replace. If you're going to have it done professionally, it could be a bit more. But again, I'll have to admit to a bit of ignorance on motherboard fans, as I've never seen one, so I'm not even sure if a person could replace it themselves. (Comments above seem to indicate that you can.)
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