The latest version of Microsoft's Windows Defender anti-malware software is able to scan for malicious code even before Windows boots, and you can run it off a CD, DVD or USB flash drive. This makes it possible to detect rootkits and other boot process malware.
The new version is available in beta now, in both 32- and 64-bit editions. You can download it from Microsoft's web site. To find out more, including the link to the download site, see: