Editor's note: Microsoft clarified its MBR rootkit removal advice after this story was posted.

Microsoft is telling Windows users that they'll have to reinstall the operating system if they get infected with a new rootkit that hides in the machine's boot sector.

A new variant of a Trojan Microsoft calls "Popureb" digs so deeply into the system that the only way to eradicate it is to return Windows to its out-of-the-box configuration, Chun Feng, an engineer with the Microsoft Malware Protection Center (MMPC), said last week on the group's blog.

"If your system does get infected with Trojan:Win32/Popureb.E, we advise you to fix the MBR and then use a recovery CD to restore your system to a pre-infected state," said Feng.

A recovery disc returns Windows to its factory settings.

Malware like Popureb overwrites the hard drive's master boot record (MBR), the first sector -- sector 0 -- where code is stored to bootstrap the operating system after the computer's BIOS does its start-up checks. Because it hides on the MBR, the rootkit is effectively invisible to both the operating system and security software.

According to Feng, Popureb detects write operations aimed at the MBR -- operations designed to scrub the MBR or other disk sectors containing attack code -- and then swaps out the write operation with a read operation.

Although the operation will seem to succeed, the new data is not actually written to the disk. In other words, the cleaning process will have failed.

Feng provided links to MBR-fixing instructions for XP, Vista and Windows 7

Rootkits are often planted by attackers to hide follow-on malware, such as banking password-stealing Trojans. They're not a new phenomenon on Windows.

In early 2010, for example, Microsoft contended with a rootkit dubbed "Alureon" that infected Windows XP systems and crippled machines after a Microsoft security update.

At the time, Microsoft's advice was similar to what Feng is now offering for Popureb.

"If customers cannot confirm removal of the Alureon rootkit using their chosen anti-virus/anti-malware software, the most secure recommendation is for the owner of the system to back up important files and completely restore the system from a cleanly formatted disk," said Mike Reavey, director of the Microsoft Security Response Center (MSRC), in February 2010.

Since then, Microsoft has added a check for the Aluereon rootkit to all security updates so that when the malware is detected, the updates are not installed.

Gregg Keizer covers Microsoft, security issues, Apple, Web browsers and general technology breaking news for Computerworld. Follow Gregg on Twitter at @gkeizer or subscribe to Gregg's RSS feed . His e-mail address is gkeizer@computerworld.com.