Rootkit is a malware that alters the operating system, and the way the operating system works. The main goal a rootkit is to hide itself and hide what its doing so that no one will ever know that its there. Once a rootkit gets in a system it is very difficult to find it, it’s whole point is to hide itself. A rootkit is able to intercept processes that the operating system performing.
The most famous and controversial case was when Sony used rootkit technology to hide their drm (copy protection) to keep their cd’s from being copied. Once you put the cd in your computer it would install itself in the background with the user consent. The worst part about this is it would allow other malware to use this Sony rootkit to hide itself. There were a number of lawsuits and Sony recalled the cd’s.
Microsoft has a tool called RootkitRevealer. F-Secure has one called Blacklight, Avg also has one. Scan your system with all of them and see if you have a rootkit on your system.