In an interview with "FORTUNE" magazine, Microsoft General Counsel and Senior Vice President Brad Smith and Vice President Horacio Gutierrez allege that open-source software (OSS) such as Linux is infringing on 235 patents owned by the software giant. And now it's time for companies and users who use these solutions to pay up, they say: Microsoft is now seeking royalties from the use of its patented technologies.

"This is not a case of some accidental, unknowing infringement," Gutierrez told "FORTUNE." "There is an overwhelming number of patents being infringed."

According to Smith, the Linux kernel alone violates 42 Microsoft patents; whereas the OS's UI violates another 65. Meanwhile, the open-source office productivity suite OpenOffice.org violates 45 Microsoft patents. Other open-source applications violated an additional 83 Microsoft patents, Smith says.

Although Linux fans will be quick to charge Microsoft with spreading FUD, for "fear, uncertainty and doubt," a more rational and useful task would be to figure out whether Microsoft's charges are legitimate and, if so, what needs to be done. Lawyers representing the free software movement--I'm assuming they're working pro bono, of course--say that software isn't legally patentable because it's just a collection of mathematical algorithms. Besides, while 235 sounds like a big number--heck, it is a big number--many of those patents might eventually be found to be invalid anyway.

Furthermore, Linux suddenly has some friends in big business. Companies such as Wal-Mart are using Linux software, and Sony, Philips, Novell, Red Hat, and NEC recently banded together to form the Open Invention Network (OIN) so that they could acquire a portfolio of patents that they could use in case a big software company tried to sue Linux backers for patent infringement. Thus, if Microsoft does sue anyone over this issue, the OIN could sue Microsoft for similar violations in retaliation. They might even get a court to force Microsoft to temporarily stop selling Windows, which could be devastating to the company.

According to the "FORTUNE" article, Microsoft has been lobbying the Linux and open-source community for patent royalties for years. Red Hat began talks with Microsoft last year, and Microsoft of course announced a deal in November 2006 with Novell, another Linux maker, in which the company agreed not to sue each other for violating each other's patents. Apparently, Microsoft had hoped that the Novell deal would serve as an example that other Linux companies would follow. So far, none have.