Heater core leaks are common in this model, more so if the wrong anti-freeze/coolant is used in the cooling system.
Problems for specific Volkswagen Jetta years:
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Newest reported 1999 Volkswagen Jetta problems
Electrical issues that are difficult to diagnose—and sometimes intermittent—are typically due to ground wiring issues. The most troublesome ground locations are under the battery or at the engine.
Throttle body failure is not uncommon and can lead to shifting issues with the automatic transmission and other drivability concerns.
Reverse gear failures and noise in the manual transmission models are common.
One or more power windows may fail. Our technicians tell us this is commonly due to a failed window regulator which will require replacement.
Shifting issues due to internal problems in high mileage automatic transmissions can be difficult to resolve without transmission replacement.