System and method for analyzing a graphical program. A graphical program is provided that includes a plurality of interconnected nodes that visually indicate functionality of the program. The graphical program includes a plurality of block diagrams arranged in a hierarchical manner, including a top-level block diagram and one or more sub-block diagrams, where each block diagram includes a respective subset of the plurality of interconnected nodes. At least one of the block diagrams includes a node that includes at least one of the sub-block diagrams. When a block diagram executes, all the respective nodes of the block diagram execute. Each node in the plurality of interconnected nodes is configured to provide graphical code coverage information when executed. The graphical program is executed, thereby generating graphical code coverage information for the graphical program indicating which nodes executed, which is then stored.