Hi! So I have an 02 is300, and whenever I shift into 2nd or 3rd there is this clunking noise in the rear of the car. I have no idea what it is! My bf says its because I don't hold the clutch in fully when I shift. BUT I do! And even when I let him drive it, it happens also. I don't think it's effecting its performance or anything, it's just bothering me because I have no idea why it does it. Sometimes if I granny shift, it won't make the clunking noise Does anyone else's 5speed do this or know what it can possibly be?

Happens to mine too, but it only occurs when i let off the clutch too quick. So i ride the slack in the pedal, just enough so i don't fully take my foot off the clutch. It was a lot more noticeable in my car when another friend drove my car and wasn't use to my MK4 supra OEM clutch kit.

OR it could be the transmission mounts slowly going bad, but i haven't inspected mine.

Sounds like a differential mount or slack in the driveline somewhere... Get it up on a rack and inspect all the rear mounting points for these parts...

If it isn't easily noticeable at first, apply parking brake with it up in the air, have it running and have someone attempt to slip the clutch into forwards and reverse while watching for slack in the driveshaft or excessive movement in the rear end...

Thanks! I'll give it a try

You should try this....drive the car in first, and floor it, and shift hard into 2nd. if you get a loud bang...your diff is loose...LOL. That's how i found out mine was loose on my BMW 325

Diff is definitely one of the possibilities, but I could add a dozen or so more...

Sounds like the differential bushings may need to be replaced.

I'll have to give that a try once my car gets back in the shop..I rear ended a truck

Did you ever get thank clunk diagnosed and fixed? I have a 2003 IS300 with the clunk from 1->2 and 2->3.