The company claims that the Linux kernel violates 42 of it patents, that the graphical user interface such as the Gnome and KDE projects fall foul of another 65, and that OpenOffice infringes 45.
Email programs account for another 15 violations and the remainder is claimed by various other open source applications.
The software behemoth didn't identify any individual patents that the software infringes upon, because that could allow open source developers to either challenge the patent or change the software to circumvent the patent.
Microsoft suggested that the number of allegedly infringed patents indicated the scope of the problem, but at least one open source advocate disagreed.
"Numbers are not where the action is," Eben Moglen, long time counsel to the Free Software Foundation and former head of the Software Freedom Law Center said in Fortune.
"The action is in very tight qualitative analysis of individual situations."
Microsoft chief executive Steve Ballmer has already warned of a forthcoming legal battle, but this is the first time that Redmond has been so specific.
"The only real solution that [the free-software] folks have to offer is that they first burn down the bridge, and then they burn down the patent system," said Brad Smith, Microsoft's senior vice president and general counsel.
"That to me is not a goal that's likely to be achieved, and not a goal that should be achieved."
However, the US Supreme Court may also have a role to play. Last week the court ruled that many patents were not sufficiently novel to be patented and it has yet to rule on the software patent issue.
The patent threat against open source community has been a hot issue over the past years challenging the very existing of such software . Patent owners such as Microsoft could file legal charges against individual users of open source software, companies supporting the products or individual developers.
The nightmare scenario would resemble that of the legal charges that SCO files against IBM and corporate Linux users for alleged copyright violations by the operating system. SCO claims ownership of the so-called AT&T Unix source code and alleges that Linux developers copied parts of the code.
The SCO case however also demonstrated the risks of a legal campaign against open source. Following the filing of its case, SCO has been isolated by several of its partners and competitors, and numerous customers have cancelled their contracts, causing its revenues to plummet.
Microsoft over the past years has been attempting to generate licence revenues from its patent portfolio. Most famously, the company last November inked a www.vnunet.com with Novell over its Suse Linux software.
Microsoft began stepping up its patent programme in 2002, the year that Smith became general council. In 2002 it filed for 1,411 but by 2004 it had risen to 3,780 and has now passed 5,000.
The company is no stranger to patent law disputes. From April 2004 through to March 2007 the company paid $1.25bn to Sun Microsystems, $536m to Novell, $440m to InterTrust, $60m to Burst.com, $6m to private inventor Carlos Amado, $115m to z4 Technologies, $74m to Korean company P&IB, and most recently, $1.52bn to Alcatel-Lucent over patents allegedly infringed by Microsoft's software.
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