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.
Problems for specific Honda CR-V years:
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Repairpal verified 1999 Honda CR-V problems
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 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.
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.
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.
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 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.
A clunking noise heard from the front suspension may be caused by the flange bolts for the upper control arm.
The rear trailing arm bushings tend to crack and break requiring replacement of the bushings.