A ground loop noise, or alternator whine. I'm struggling to completely eliminate it in my car as well.
It is very hard to solve with only a little information, but you need good ground connections, good RCAs, the RCA cable(s) should be "far" away from the power wire. If it is minor, a ground loop noise suppression device will work (Monster Cable makes a pretty decent one, but it isn't the cheapest - I think it is about $40). However, it will not remove the noise if it is really noticeable.
Sorry I can't be more help. Otherwise, if you have plenty of power, turn the gain down on the amplifier. That will help tremendously (but of course means you get less volume). Decks with high (4V or more) preouts help as well. Don't know what you have for a deck.