System and method for debugging a graphical program deployed to hardware. The graphical program may be received. The graphical program may include a plurality of nodes and connections between the nodes which visually represents functionality of the graphical program. A hardware description may be generated based on the graphical program. The hardware description may describe a hardware implementation of the graphical program. The hardware description may be deployed to the programmable hardware element and the programmable hardware element may be executed. The graphical program may be displayed on a display of a host computer system that is coupled to the programmable hardware element. Debugging information may be received from the programmable hardware element during the executing. The debugging information from the programmable hardware element may be displayed in the graphical program displayed on the display. The displayed debugging information may be used to debug the hardware implementation of the graphical program.