A method and system for comparing compound documents. An original compound document and a modified compound document are analyzed to determine and mark the location of embedded objects. A comparison is performed between an original primary document and the modified primary document, ignoring the embedded objects, the output of which is a comparison output document. The embedded objects are compared by copying the contents of the embedded objects to compatible documents, comparing the embedded object from the original compound document and the embedded object from the modified compound document, the output of which is inserted into the comparison output document using the location markers of the embedded objects.