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alright so i have been driving for about 14 months with this noise that i cant seem to figure out. Basically i drive a 5 speed manual civic ex and when ever im reving between 2500-3200 rpms there is kinda like a rattle or chatter not so much a knock, but i guess you can put it that way. anything before and past those rpms and the noise is not there anymore. Also i have to be about 1/4 throttle and thats when it is the worse, more than that and the noise seems to be gone sort of unless the engine noise just hides it. Now i did it in neutral and i cant seem to hear it so only under load. Now ive been trying to figure this one out but i cant. piston slap, injectors, exaust leak etc. I did some research and those were my ideas but i want to see if anyone can really tell me where that sound comes from? the sound has not gotten any worse so i dont think its a knock.

 
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Check for rusted/loose exhaust shields.

 
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My car doesnt have exhaust heat shields cause it has after market header and exhaust pipe. Any other ideas. I also read up that it could be detonation. PLEase help!

 
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I have a bad input-shaft bearing in my '05 5spd that acts a similar way although I can hear mine at idle, it's just very subtle. If your exhaust is loud it could be hiding the noise, I have a stock exhaust and can barely hear it at idle.

With the car idling get on the ground and stick your head down by the transmission, have someone push and hold the clutch for 5s or so, then release it, do it a few times and see if you can hear a very soft version of the noise.

If it's an ISB it will make noise when the pedal is out, then stop when you push on it.

 
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Anibis i think you might right on the spot there. So when the clutch is pressed in on idle there is like a weird noise i can barely hear under the car. the worst is in 1st and 2nd gear around 2500-3000 rpm is when i can really hear it. After that you cant even tell anymore. How long could i be drving with an input shaft bearing like this. Also in august of 2011 i bought a clutch kit and had it replaced. The sound was there before and was still there after. The sound has not gotten worse and shifting is smooth and easy and car runs strong. So how long could i be driving like this? Could i go till december when i plan on selling the car