The AC compressor may seize resulting in loss of cold air from the AC vents. Often when the compressor fails in the fashion, debris is spread through out the entire air conditioning system resulting in very expensive repairs.
Problems for specific Honda CR-V years:
Car problem reports
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Most reported 1999 Honda CR-V problems
A groaning noise from the rear differential heard while going through turns can be caused by differential fluid break down. Servicing the rear differential will generally correct this concern.
The front brake rotors can warp and cause a vibration when braking. The rotors will need to be machined or in cases where they are worn to thin, replaced to correct this issue.
Worn door lock tumblers can cause the door lock to be sticky or not work at all. The lock has to be removed and the tumblers need to be replaced for this issue.
A faulty brake master cylinder reservoir filter can cause the brake system indicator to illuminate after a cold start and then go off. Replacement of the reservoir filter will commonly fix this problem.
The rear trailing arm bushings tend to crack and break requiring replacement of the bushings.
The engine valves can prematurely fail. The cylinder head will need to be replaced due to wear in the area where the valves seal. Intake or exhaust valve failure may illuminate the Check Engine Light. The car may have poor engine performance and fail emission tests.
A clunking noise heard from the front suspension may be caused by the flange bolts for the upper control arm.
Some vehicles with an automatic transmission can have an issue with a harsh shift from first to second gear. Honda has released a service bulletin suggesting to flush the transmission using Honda ATF-Z1 and replace the linear solenoid. If that does not cure the problem the fault is internal and the transmission will require replacement or overhaul.
Honda issued a recall of 1998 and 1999 models to inspect and repair the wiring harness under the dash and install a piece of tubing to protect the harness. Various electrical issues can develop if these wires have been damaged.
A worn speed sensor drive gear can cause a surge when using cruise control and illuminate the Check Engine light. Transmission replacement will be needed.