Joern Wettern at Redmondmag has a good overview of the situation.
As if there weren’t enough threats coming at you via the Internet, now you have to secure your systems against rootkits, as well. Rootkits are similar to spyware, viruses and worms in that they’re designed to run on your computer without your knowledge. Once on your system, they often perform a malicious task, like creating a backdoor to enable unauthorized access to your system.
What makes rootkits unique is that they’re designed to avoid detection by standard scanning methods and tools. If a rootkit has installed itself on your computer, you won’t find it using Windows Explorer or see it in the list of services that are currently running. Most virus scanners can’t even find a typical rootkit. To protect yourself against this type of threat, you need to know how they work and how to remove them from your systems.