01 civic. Only hear it when my car is running. I checked all my speaker wiring. Is it my alternator? Or something else?

 

Most likely alternator noise...

Do you have a factory system or after market?

Best things you can start with is making sure you have STRONG grounds, I generally re-wire my grounds to my head units anyways just to make sure, obviously considering this check your main chassis grounds and battery connections as well.

You can also throw a small capacitor inline with your main power lead to your head unit, that can help filter a bit. If you can you want to stay away from actual "Filters" if you are a SQ nut, if not they can work wonders.

If you are running amps, make sure your gains are set properly as with them all cranked up you can easily pickup noise from your signal cables...

*Boy wouldn't it be nice if they just all used balanced signals....*

 

Aftermarket system. 2 amps. One to the deck and inside speakers and one for the subs. The whine is only there when my car is running and the radio is on. I checked all my grounds and both gains on the amps. The system has been in for over 2 years and it just started about a week ago. Sorry I wasn't more specific to start.

 

It could be an internal issue with the amp (filter or some other circuit went out) if everything else is the same and looks good

 

Also check your RCA wires. Make sure they are not running parallel with the power wires. If they are too close to each other, they could cause engine whine.