A rootkit virus hides within the Windows OS and tries to avoid being found.
The problem came to light in February, as security updates issued caused machines that had been infected with the rootkit to continually crash the system.
This rootkit was identified as Alureon. It can pluck out usernames, passwords, credit card details etc from a system and send the details to the hacker. It can also leave a backdoor open and allow the hacker access to the system.
New updates from Microsoft can now spot if a system has been overtaken by the Alureon rootkit and stop the update installation. The updates also remedy problems in the kernel or core of the operating system, which is where the rootkit is found.
Microsoft is hoping that this will give owners confidence and continue to install updates. The fear is that some owners may stop updating, due to a fear of making their system crash.
It is not yet clear how many owners have been affected.