Although Windows XP support ended on April 8, 2014, updates for the Windows XP version of the Malicious Software Removal Tool would be provided until August, 2016 version 5.39. Starting with version 5.1, released on June 11, 2013, support for Windows 2000 was dropped altogether.

The last version of the tool that could run on Windows 2000 was 4.20, released on May 14, 2013. Since support for Windows 2000 ended on July 13, 2010, Microsoft stopped distributing the tool to Windows 2000 users via Windows Update. The tool is also available as a standalone download. Since its January 13, 2005, Microsoft releases the updated tool every second Tuesday of every month (commonly called ' Patch Tuesday') through Windows Update, at which point it runs once automatically in the background and reports if malicious software is found. Outside its monthly deployment schedule, it can be separately downloaded from the Microsoft. It scans its host computer for specific, widespread malware, and tries to eliminate the infection.

First released on January 13, 2005, MSRT does not offer real-time protection. Microsoft Windows Malicious Software Removal Tool ( MSRT) is a freeware second-opinion malware scanner that Microsoft's Windows Update downloads and runs on Windows computers each month, independent of the install antivirus software.

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