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I have repaired this hard to diagnose problem by draining and refilling the cooling system with clean water, then refilling again and running the engine with clean water, then back-flushing the heater core until I had good flow again, then draining the water from the cooling system and refilling with new coolant. Heat works again. The alternative is a $300 heater core and 6.6 hours of labor. At a shop this averages about $900 for the job. Other issues that can also affect this problem are: Low coolant? Bad thermostat? I had the same problem, I had hot water flowing through the heater core, blower blowing cold air. I found that the glove compartment was keeping the air controller from moving to open the air controller flap. After I removed the glove compartment it started working, then I put it back together and it still works.

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Q: 2001 vw passat no heat coming out of vents got a coolant flush still no heat help?
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