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1999 Civic HX Noise that only goes away when i press the clutch in

My 99 civic HX (manual trans), makes a noise that is there on start up and while the car is running. It only goes away when I press the clutch in. Any Ideas?

Check the fluid level in the transaxle.


Do you mean the manual transmission fluid?



A throwout bearing or pilot bearing about to go bad. The only fix is to remove the transmission to expose the clutch. May as well replace the clutch while you are there.

BustedKnuckles: So is a throwout breaking or pilot bearing the same thing? I know when you replace a clutch, that you usually replace the throwout bearing, pressure plate, and clutch disc. Also is it common for the bearing to be making noise at 110,000 miles?

The pilot bearing and the throwout bearing are two different animals. The pilot bearing is inside the center of the flywheel and supports the transmission input shaft. The throwout bearing presses the clutch fingers and takes the pressure off the clutch so you can shift the transmission. A bad throwout bearing at 110K is not uncommon and many fail sooner than that.

The car does not make noise when in gear and while the engine is under load? Could this still be a clutch issue?

Both the throwout bearing and the pilot bearing will make noise when the clutch pedal is pushed down so your problem is unlikely to be those items. Have you checked the transaxle oil/fluid level as Tester recommended?

You haven’t really described the noise. Is it a whine, a roar, a grind, a rattling, a rumble, a squeek, etc.? Be as descriptive as you can. How many miles on this transaxle and the vehicle?

Hopefully, the problem is not in the transmission $$. Hope we can help narrow this down.

@lanedans1 - now I’m confused. FIrst you said the noise oily goes away when you press the clutch, then you said “The car does not make noise when in gear and while the engine is under load?” Which is it?

I’ll bet a box of honey doughnuts that this turns out to be the throwout bearing. The TB is a thrust bearing, and can easily make noise when under thrust load (clutch in) that disappears when the load does (clutch out)

OR can make noise when freespinning (clutch out) and not when loaded (cllutch in).

Honey doughnuts? Anyone?

To the OP; do you know how many miles this clutch assembly has on it? That could be a clue.

So the car with 110k on the clock does not make noise when the car is under load moving or when the clutch is pressed in. I’m just not sure what is wrong.

I Agee with TSMB and others. My guess is the throwout bearing.

Thank you all very much for your help and comments. I am going to just replace the throw out bearing, pilot bearing and clutch. Thanks

Remember we’re only able to go off of your comments. A good mechanic driving your car is the one to trust.

I’d suggest you also change the pressure plate assembly. If you do it yourself, a “kit” should include everything you need including the pilot shaft. The pilot shaft is a tool used to align the clutch plate when the pressure plate assembly is bolted over it, such that when the tranny is then mated to it everything will line up properly.

It’s a bad bearing inside the transmission. When you depress the clutch, the throw-out bearing is spinning and under load…When you release the clutch, the throwout bearing is not spinning…Now the transmission mainshaft and countershaft are spinning and a bearing supporting those shafts is making the noise…That’s why Tester said check the transmission lubricant level…

The throwout bearing is on the tranny input shaft. Whenever the tranny input shaft is spinning, the inner race of the TO bearing is spinning. The difference between having the clutch in or out is that with the pedal in, the bearing’ is thrust loaded, with the pedal released the bearings outer race, cage, and bearings are frewheeling, free to spin or rattle as they choose.

The throwout bearing is NOT mounted on the transmissions input shaft…The only thing connected to this shaft are the internal transmission gears and at the input end, the clutch disk…The bearing is mounted on a moveable fork and is guided by sliding over a stationary support which fits over the mainshaft…With the clutch pedal released, no part of the throwout-bearing should be moving.

The very end of the transmission mainshaft is supported by the pilot bearing which is mounted in the end of the engines crankshaft. If THIS bearing fails, the noise and symptoms become more complicated…

Listen to Caddyman. You say it yourself, the noise goes away when you press on the clutch pedal. This is when the throwout bearing is engaged and spinning. No noise because you have stopped the trans shafts from spinning. The input shaft bearing is the most common failure in this trans, it is the 1st bearing on the mainshaft, but all the bearing should be checked for damage.