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Not enough hot air

I have a 1999 GMC Sonoma with 76,000 miles. The heater started blowing cold air so I took it to my local GMC dealer and they did a chemical flush of the heater core. The heater now blows luke warm air but it is not nearly as warm as it used to be. My local dealer repair shop is now telling me that I need to replace the heater core itself to the tune of about $1,000. Do I have any other options?

This is not an uncommon issue for older cars.
What I recommend is that you try to fix it yourself, and here’s what I would do.
Put a large pan or tub under the firewall area.
Locate the two heater hoses on the firewall. It’ll be fairly obvious which ones they are.
Disconnect both hoses.
Try to flush the heater core out yourself using a simple garden hose. It may take quite a while.
Flush it out from both sides, until you get a good clean flow out from both sides.
If you see chunks of “sand” coming out, that is the degraded Dexcool coolant.
I’ve had some luck doing this on different kinds of vehicles.
I know you’ve already been to the dealer, but sometimes patience is what’s required.
You’ve got nothing to lose at this point.

Is your coolant at regular operating temperature?
Is the upper radiator hose hot?

If I replace the heater core will that fix the problem or is a possibility that it wi be a waste of money?

I have also replaced the thermostat.

Replacing the thermostat was a good move.

On Monday I blasted out a plugged heater core on a 2001 GMC Sonoma 4.3. Same thing as your truck.

This is what I used. It took just a few minutes. As I said before, I’ve done it this way before, with good success. One of the earlier cars I fixed this way was a 1998 Chevy S10 4.3

http://www.sears.com/craftsman-10-pattern-front-trigger-nozzle/p-07169153000P?prdNo=1&blockNo=1&blockType=G1

Replacing the heater core will cost a lot more money, even if you do it yourself.

And if my way doesn’t work, you still have that option.

And by the way, all of those cars are still running, blowing hot air, and the heater cores haven’t leaked. And all of them have racked up some time and miles on them since my repair.

I will say it again: Try to save that $1000 and fix the truck my way, even if you have to pay somebody a few bucks to do it. I think you can do it yourself. It’s not difficult.

My first suspect is blend doors not working as they should. Do you get full heat if defrost is off?