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I've been having this problem with my 2005 civic where the heater will only work intermittently. Once the thermostat gets up halfway, to the point where the heat will usually be OK to turn on, sometimes it blows hot but other times it'll blow cool (not freezing cold outside air, it still feels a tad bit heated). I can't really seem to find any connection between stepping on the gas, the brake, letting the car run longer, etc. It just seems sort of random and it usually goes back and fourth between full-on heat and cool air every few minutes or so... I'm kind of stumped here. Any thoughts?

 
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There are some other similar threads to your problem try searching. Start off by checking the coolant level in the radiator. If it is low, I would check in the reservoir and inspect the level. If it's above the MAX mark, you either got a head gasket on the way out or a "stuck" thermostat which I doubt is your problem.

Also another thing to check when the engine is up to operating temp. There are 2 hoses that go through the firewall into the dash area. Turn the Temp Control to the hottest setting and turn the blower/fan a couple of clicks. Then Grab the hoses and see if they are warm. If one is warm and the other is cool then you probably have a clogged heater core or heater valve.