The catalyst for Stallman's position was the inclusion of Tomboy note-taking software into an unstable branch of Debian. Many developers feared that Microsoft may lay licensing claims against Mono. These developers have now got some prominent protection in the form of Richard Stallman in an article on the Free Software Foundation (FSF) website. Stallman considers Debian's decision to include Mono to be moving in a "risky direction," with Microsoft possibly using patent claims to "force all free C# implementations underground some day." Thus he warns not only against implementing Mono, but also C#-based software. Should the case arise of "losing the use of C#," all applications based on it (such as Tomboy) will also be lost. "That doesn't make them unethical, but it means that writing them and using them is taking a gratuitous risk."

Ubuntu users have long been discussing this issue, but with a different response from Ubuntu. Colin Watson summarizes the position of its technical board on the issue as, "there appears to be no significant cause for concern." "In the case of Mono," he goes on, "Canonical (who would bear most of the liability for any violation) does not currently believe this to be a major risk, as should be evident from the fact that it has been shipped in Ubuntu main since 5.10 and in the default desktop since 6.10." The selection of Mono applications were introduced, allegedly, based on their merits, but "were there to be an issue, Mono would be easy to extricate... In short, Mono is currently well-maintained in Ubuntu...."

Stallman has a much different view and his appeal is quite clear: "In other words, we should discourage people from writing programs in C#. Therefore, we should not include C# implementations in the default installation of GNU/Linux distributions, and we should distribute and recommend non-C# applications rather than comparable C# applications whenever possible."