Boot off of your Windows disc. Depending on if it's an XP or Vista/7/8 disc, it's a bit different.
For XP, you need to go to the Recovery Console; so just press R when you're onthe initial screen for the XP setup.
For Vista/7/8, after you select your language, there should be a link that says "Repair my computer" on the screen with the Install Now page. Click the link, and it should take you to a new window where you can open up a Command prompt. Run this command:
chkdsk c: /f /r
It will go through 5 stages (could take a while depending on the size of the drive) and mark off any bad sectors.
After that, I would recommend formatting with NTFS using a GParted LiveCD, as it's formatting technique is much better than Windows' IMO.
Then install Windows on the drive.