It would help to know your full system specs, what OS you're running, etc. You haven't provided enough information to help divine a solution to your problem.
Some IDE drivers can cause this, or if your drive isn't operating in DMA mode. Software like Intel Application Accelerator can cause this, as well as certain nVidia IDE drivers. A fragmented hard disk could be an issue, or buggy chipset drivers. The list goes on, but without enough information, there's no way to point you to a solution.