Is it normal for my '99 YZF R1's (12 000miles) gearbox to sound a bit clunky when I shift from 1st to second?

My ZX 9R did the same but that bike's gearbox was knackered.

The R1 is still under warranty btw.

Answers:
I actually don't think it is all that uncommon to have notchy shifts from 1st to 2nd. It isn't GOOD - but it isn't unusual. There is the greatest difference between the speed of internal transmission bits when shifting from 1st to 2nd. To avoid it make sure that you're changing gears at the manufacturer's suggested shift point. I was noticing a notchiness between first and second on my KLR650 but if I shifted a little earlier was totally smooth. Also, make sure it's a firm shift - if you're hesitant going from first to second, you will occasionally feel neutral as you pass through it.
That said, it never hurts to have the dealer check it out. Warranty coverage of transmission problems can be shakey though because many problems in the gearbox are the result of operator error and not a defect.
Good Luck!
No..it's not normal. I think personally you should get a girlfriend who is chubby, and it will all balance out. Trust me.
No it's not. You should take it to a YZF dealer immediately!!
I'd bring it in or at least ask about it at the dealer. I still has that warranty and I'll assume you didn't do anything to break it, so why not? No cost to you.
Not normal. Have you been getting the oil changed at 4000 mile intervals? Also don't let it coast as that will overheat the gearbox. If it's under warranty take it to the shop and have it checked.if there are loose bits in there they will eat the tranny in a couple of hundred miles. Chill with the burnouts too.
Go have them check your clutch, R1'a and R6's are known for going bad early, I had good luck with my first one, but on the second r1 I had, I had to upgrade to a better clutch, was well worth it
git it fixed under warranty asap. 1st gen R1's came stock with weak dogs on the trans gears that were fixed free under a voluntary recall. Story is a couple guys got hurt bad when the dogs rounded off at high revs and caused the engine to sieze.
If you've been a little 'enthusiastic', with your changes,or your launches, you've possibly done some damage to first, and second, as the strain is greatest, down low in the box. Take it back, and get it looked at. It's a truck load of $$$$$$$$ , if it gives up, and roots the entire box, at 10,000 revs !!!

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