Differencing and merging tree-structured documents, such as eXtensible Markup Language (XML) documents, is disclosed. A differencing-and-merging system for tree-structured documents of one embodiment of the invention includes a difference processing unit and a merging processing unit. The differencing processing unit performs a difference operation on at least two tree-structured documents, in accordance with difference configuration information regarding the documents. The merging processing unit performs a merging operation on the tree-structured documents from correspondence information generated by the difference processing unit, based on the difference operation configuration information regarding the documents. The correspondence information indicates differences among nodes of the documents. The difference operation configuration information specifies one or more nodes among the documents that are to be considered equivalent when the difference operation is performed, and one or more nodes among the documents that are to be ignored when the difference operation is performed.