Embodiments of the present invention include a computer-implemented method of comparing computer documents such as programs and XML. A hierarchical level may be specified. For each hierarchical level between a root and the specified hierarchical level, first and second searches are executed for nodes representing subsections of each document. The returned nodes from the first search correspond to subsections of the first computer document, and may be set equal to nodes representing the second document if the addresses are the same. The second search is executed on the second document, and the addresses of the nodes returned by the first search may be compared against addresses for nodes returned from the second search. Nodes are matched and marked as equal. The hierarchical level may then be increased and the process repeated until the root node is reached.