codice:
import javax.xml.parsers.*;
import org.w3c.dom.*;
import java.io.*;
import org.xml.sax.*;
import javax.xml.transform.*;
import javax.xml.transform.dom.*;
import javax.xml.transform.stream.*;

            TransformerFactory transformerFactory = TransformerFactory.newInstance();
            Transformer serializer = transformerFactory.newTransformer();
            serializer.transform(new DOMSource(document), new StreamResult (new FileOutputStream(source)));
dove "source" è il percorso del tuo file