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Experience:  ASE Master Auto Technician for 5 years, ASE Refrigerant Handler, ASA, iATN
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Echo: My 1.3L 2003 Toyota echo started over heating awhile

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My 1.3L 2003 Toyota echo started over heating awhile back, so check and found that the thermostat wasn't opening at preset temperature, so replaced it.
The car still continued to over heat from losing water.

I pressure tested the cooling system cold to 100 kPa which it held for 20 minutes without dropping and without any external leaks.
I then proceeded to start the engine and found that the pressure rose rapidly. After repeating this test a couple of times, I came to the conclusion that there was a combustion leak and proceeded to remove the head.

My Problem is, the head gasket shows no compromise between combustion chambers and water galleries. Both the head and block faces are straight and after completing a die penetration test the head face show no cracks.
What am I missing?
The test you did is not a good way to see if there is exhaust gasses in the coolant. There is a block test kit you can get that will tell you that.
The pressure normally rises when you start the vehicle. Since the thermostat is closed there will be some pressure in the system, but since you already had pressure on the system then it would rise much quicker.
There are several things that might be causing this problem.
You might not have had the system all the way full of coolant. I know this seems ridiculous but you would be surprised at how many people do work on their cooling system and don't follow the correct procedure to get the system completely full.
There could be a leak that only leaks under very low pressure. Sometimes putting pressure on it will only cause the leak to seal up and make it look like there isn't a leak.
I've seen several times, leaks that only started leaking when the vehicle was being driven. There were no other signs of leakage. This was usually caused by a faulty water pump.
It's also possible that you simply had and air pocket in the cooling system and that was causing the overeating.

A good test to do once you get it back together and have the cooling system full is to put tracer dye in the cooling system and run it for a few miles (enough to get the engine fully hot), then use a black light to see if you can see where the coolant is leaking.

Since you see no signs of leakage with the engine apart it is very unlikely that there is any internal coolant leakage.
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