I have Linux on my computer as well, but this concerns both versions of Windows I have. They both share the first of my two hard disks, with the first partition being a 10gb FAT32 (with Microsoft Windows 98 Second Edition). The second parition is roughly 70gb NTFS, and contains Microsoft Windows XP Home Edition Service Pack 2.

I've been defragmenting the NTFS partition every time Disk Defragmentor tells me I should, but I've left the other partition alone. The reason is that I still don't fully understand how defragmenting works, and I don't know if defragging in one OS will break the other. I really don't care if Windows 98SE is slowed down, since I don't do anything with it other than play ancient games, but if it doesn't work anymore, that's a different story.

I analyzed the FAT32 partition today, and it appears to be badly fragmented. I'm wondering if it's ok to defragment it with XP. Is it? Will it affect Windows 98? Is there the possibility that it will affect Linux, which is sitting on a second hard drive?

Defrag away!

You can do the defragmenting of your windows 98 partition using the defragmenting program of Windows xp. There is no problem. This is because of the fact that windows xp understands FAT32 partitions and will do the job nicely.

yeah and it doesn't do any harm to linux partition neither. defragmentation is used only for arranging your disk clusters on purpose your os working faster with files which are situated on HD.