It is useful to understand the corresponding relationships between each part of related documents, such as a conference paper and its modified version published as a journal paper, or documents in different versions. However, it is hard to associate corresponding parts which have been heavily modified only using similarity in their content. We propose a method of aligning documents considering not only content information but also structural information in documents. Our method consists of three steps; baseline alignment considering document order, merging, and swapping. We used papers which have been presented at a domestic conference and an international conference, then obtained their alignments by using several methods in our evaluation experiments. The results revealed the effectiveness of the use of document structures.