System and method for debugging a graphical program. A graphical program may be received, e.g., from storage, from another process or device, etc. The program includes parallel graphical program portions, each portion including a graphical program structure and/or an execution path in the graphical program. A first graphical program portion of the parallel graphical program portions may be single step debugged, including executing the single step in the first graphical program portion, and executing, in the background, code in each of the other graphical program portions that is scheduled to execute between start and end of the single step in the first graphical program portion.