Mono’s implementation of those components of the .NET stack not submitted to the ECMA for standardization has been the source of patent violation concerns for much of the life of the project. In particular, discussion has taken place about whether Microsoft could destroy the Mono project through patent suits.
The base technologies submitted to the ECMA, and therefore also the Unix/GNOME-specific parts, may be non-problematic. The concerns primarily relate to technologies developed by Microsoft on top of the .NET Framework, such as ASP.NET, ADO.NET and Windows Forms (see Non standardized namespaces), i.e. parts composing Mono’s Windows compatibility stack. These technologies are today not fully implemented in Mono and not required for developing Mono-applications. Richard Stallman has claimed it may be "dangerous" to use Mono because of the possible threat of Microsoft patents.
On November 2, 2006, Microsoft and Novell announced a joint agreement whereby Microsoft agreed to not sue Novell’s customers for patent infringement. According to Mono project leader Miguel de Icaza, this agreement extends to Mono but only for Novell developers and customers. It was criticized by some members of the free software community because it violates the principles of giving equal rights to all users of a particular program (see Novell and their Patent Agreement with Microsoft).