XML data integration tools are facing a variety of challenges for their efficient and effective operation. Among these is the requirement to handle a variety of inconsistencies or mistakes present in the data sets. In this paper we study the problem of integrating XML data sources through index assisted join operations, using notions of approximate match in the structure and content of XML documents as the join predicate. We show how a well known and widely deployed index structure, namely the R-tree, can be adopted to improve the performance of such operations. We propose novel search and join algorithms for R-trees adopted to index XML document collections. We also propose novel optimization objectives for R-tree construction, making R-trees better suited for this application.