Most file systems will have some degree of fragmentation. A fragmented file is one that uses blocks on the hard disk drive that are not consecutive. A consequence of fragmentation is that when a file is read, the hard disk needs extra seek time and rotational delay. This translates to less performance, regardless of the available processing power, memory, input/output bandwidth.
Different file systems use different strategies to minimize the effects of fragmentation. In addition to counter-fragmentation strategies, some file systems also have tools to defragment a hard disk. In the ideal case, a defragementation tool runs on a live system to minimize down time.