There's two types of fragmentation with file systems: file fragmentation and drive fragmentation.
HFS+ is not perfect (though better than NTFS) at always placing the right file in the right place and keeping all the linkages close to each other on the disk.
Fragmentation does happen, especially if you use the same install of a system for a long period of time. iDefrag is a real decent program to use once in a while, I've found.