More and more sys admins are realizing the danger of rootkits. However, I've known only a few, who spent enough time to estimate how big the threat really is. Since the main purpose of rootkits is to hide themselves from users and sysops, you usually don't know of them. I guess there are not many Windows administrators out there, who never had problems with computer viruses. But how many ever realized that they have rootkits in their network?
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I must admit, I am one of those who neglected this topic for quite a while. At least, I googled about it now. Originally, I wanted to make a list of anti-root tools. But then I found Antirootkit.com. They have a comprehensive collection of anti-rootkit tools plus some useful information like a list of articles and of known rootkits.
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I have read some reviews about Sysinternals RootkitRevealer a while ago. I suppose, it is the most prominent among the anti-rootkit tools for Windows and it is free. So I would start with this tool first.