When the clutch is engaged, I hear some type of rattling from the tranny. When the clutch is not engaged, everything is normal. Is it the throw out bearing, or something more major?

 

You guessed it, throwout bearing...Slim possibilty it could also be the pilot bearing, especially if the "noise" gets louder the longer the clutch is held in

 

yeah i'd say replace those bearings. Did the car just have the clutch/fly replaced?

 

clutch engaged, as in your foot is off of the pedal? If you're hearing some ticks and rattles aka "rocks in the box" while cruising around, your tranny could be toast

 

First - check the tranny oil level, before it gets worse.
Look for leaks.

Is the noise random? (box of rocks)
Or is it rythmic? (one tick per engine rev)

 

same thing happened to me and my pilot was shredded

 

It is pretty random. It happened the past 2 days, and did it a while before. When I said engaged, I meant while I was pressing the clutch, my foot on it, sorry. Also, I revved out first gear today while merging into traffic, I heard it pretty loud agian. It is actually the first time I heard it while I was moving. As far as I know, it is stock clutch and fly. The car has 56,000 miles on it.

 

I posted this up a while ago, but just to follow up on it, I figured since I was going to take the tranny down, I'll replace the entire clutch. It was the pilot bearing. Pieces of it fell everywhere when I took the tranny down. I the clutch was still good, but I replaced it anyway. When it was back together, the noise went away. So, Csefiroth0, we had the same problem.