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I recently bought an 04 Civic EX with a manual five speed. While driving it yesterday I noticed that if you leave your hand on the gear shift you can feel a vibration in 3rd and fifth gear. In the other gears you can't feel anything. Are third and fifth gear riding on the same shaft? Could this be a sign of a bearing going out, or is this pretty normal. I can't tell if it is makeing any noise, because the tires that are on it are worn badly and they roar. I am putting new tires on tommorrow. As far as shifting the tranny feels great.

 
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I have a little better description of the issue after driving it to work today. It does not make any noise at all. If you are in 5th gear and push the shifter forward you can not feel any vibration. If you release the shiter and just put your hand on it you can feel the vibration. If you put a little pressure pulling it back, it gets worse. Also it is barely noticable until you hit 60 mph. Does anyone elses car do this? Maybe it is normall. I hope so.

 
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Sounds normal to me. Put the car in fourth gear and apply a little pressure upwards while driving and you will feel it too. That's why it goes away when you push it up a bit in fifth. It's just the gears doing their thing. Just means the shifter isnt going far enough to clear the vibration, but it is in gear just fine. I wouldnt worry about it.

 
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If I push forward while in 4th gear it just barely does it, but nothing like it does in 5th and 3rd gear. I guess I will just drive it until it gets worse. I may check the shifter linkages to make sure nothing is restricting it, but it goes in to gear fine, and does not pop out.

 
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I Guess this is ur first manual car.. Yes, its normal... Aint nothing wrong with ur car..

 
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I agree. If the car is not running rough or shifting rough forget about it. If your really worried about it change the tranny oil.

 
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Tranny oil in a manual tranny?? Hmm.... Never heard of that..

 
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It has to have something to lubricate it It just does not use ATF it uses MTF and requires less frequent changes.

 
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Yea, but i never heard of someone changing the oil in manual tranny, Except when u are doing tranny rebuild or clucth... I know there is oil in there but i dont think its easy to change it on our manual civics.. Or is it?

 
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It's a bit of a process. I believe in our manual it says to change it at 100k miles. There are 2 plugs on the transmission. A drain plug and a fill plug. They are both kind of on the side of the transmission. The fill plug is harder to get to than you think, so you need either a hand pump or a long, bendable funnel. The problem is you can only drain about a quarter of the fluid at one time. If you really want to change just about all of the fluid you would have to change it once, drive around a lil' while, and repeat... 3 or 4 times. You just fill the fluid until it starts pouring out of the fill plug, thats how you know the tranny is full.

 
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This isn't my first vehicle with a manual tranny, but it is the first car I have owned that has one. I will probably do as suggested and change the oil. The car has 96,000 on it and the tranny oil was changed by the dealer at 60,000. Thanks for all of your replies.