Microsoft Corp. security researchers are warning about a new generation of powerful system-monitoring programs, or "rootkits," that are almost impossible to detect using current security products and could pose a serious risk to corporations and individuals ... The malicious snooping programs are becoming more common and could soon be used to create a new generation of mass-distributed spyware and worms
Rootkits are very sophisticated monitoring systems that can hide completely within the framework of Microsoft and Linux Operating Systems. Developing rootkits requires extensive knowledge of the Operating System, so that rootkits can communicate with kernel transparently. You can think of rootkits as “Super Spyware”.
Currently we are seeing a number of viruses that carry secondary payloads that can sometimes be more dangerous than the original virus. Thus a virus could carry or download a root kit and install it transparently onto the system. With few cleaning or detection tools available the root kit could go undetected allowing malicious individuals to monitor system activity or access sensitive data.
Computerland article: Microsoft on RootKits: Be afraid, be very afraid