A system and method for automatically generating a graphical program from a prototyping environment application. By utilizing an application specialized for developing solutions to problems in a particular domain, i.e., a prototyping environment, a user may develop a solution to a problem, i.e., a prototype. The prototype may comprise a series of functions that form an algorithm or process. Once the user has developed the desired prototype, the user may request the prototyping environment to automatically, i.e., programmatically, generate a graphical program implementing the prototype, e.g., in order to run the program independently of the prototyping environment. In various embodiments, the prototyping environment may be operable to generate any of various types of graphical programs. Once the graphical program has been generated, the program may be modified as desired, e.g., in order to include features not available from the prototyping environment that generated the program.