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With the advent of native and XML enabled database systems, techniques for efficiently storing, indexing and querying large collections of XML documents have become an important research topic. This paper presents the storage, indexing and query processing architecture of eXist, an Open Source native XML database system. eXist is tightly integrated with existing tools and covers most of the native XML database features. An enhanced indexing scheme at the architecture's core supports quick identification of structural node relationships. Based on this scheme, we extend the application of path join algorithms to implement most parts of the XPath query language specification and add support for keyword search on element and attribute contents.