In November 2006, Microsoft and Linux distributor Novell inked what was to become the first out of a multitude of Windows and Linux interoperability and intellectual property assurance agreements. The Redmond Company has placed interoperability at the center stage of all Windows - Linux agreements, however, objections were raised by the free and open source community over the intellectual property assurance aspect of the deals.

Following the agreement with Novell, Microsoft announced that fact that it was opened to similar partnerships. The Redmond Company got its first firm no from Red Hat. In response to the Microsoft and Novell patent deal, Red Hat stated that "an innovation tax is unthinkable. Free and open source software provide the necessary environment for true innovation. Innovation without fear or threat. Activities that isolate communities or limit upstream adoption will inevitably stifle innovation."

But other Linux distributors did follow in Novell's footsteps. Microsoft applauded agreement with Xandros, and Linspire. Again placing emphasis on interoperability, the deals are also designed to offer patent protections to Linux users. In May 2007, Microsoft General Counsel Brad Smith and Vice President of Intellectual Property and Licensing Horacio Gutierrez claimed that free and open-source software violates on 235 Microsoft patents, with the Linux operating system and OpenOffice as the main targets.

However, neither the additional agreements, nor the patent violation treats have impressed Ubuntu Linux distributor Canonical. Ubuntu's Chief Executive Officer Mark Shuttleworth revealed that Ubuntu has declined to even discuss a potential agreement with Microsoft "under the threat of unspecified patent infringements." In this context, Shuttleworth has joined Red Hat's position in welcoming interoperability but saying no to patent protection.

"The Ubuntu community, we believe that the freedom in free software is what's powerful, not the openness of the code. (...) All the deals announced so far strike me as "trinkets in exchange for air kisses". Mua mua. No thanks," Shuttleworth concluded.