Document doc = ...
TransformerFactory tFactory = TransformerFactory.newInstance();
Transformer transformer = tFactory.newTransformer();
DOMSource source =  new  DOMSource( doc );
StringWriter sw =  new  StringWriter();
StreamResult result =  new  StreamResult( sw );
transformer.transform( source, result );

saveFile( "some_path", result.toString(), "windows-1251" );

...

     public   static   void  saveFile( String path, String data,
                                 String encoding )  throws  FileNotFoundException,
                                                          UnsupportedEncodingException,
                                                          IOException {

        FileOutputStream fos =  new  FileOutputStream( path );
        OutputStreamWriter osw =  new  OutputStreamWriter( fos, encoding );

        BufferedWriter buffWriter =  new  BufferedWriter( osw );
        buffWriter.write( data );

        buffWriter.flush();
        buffWriter.close();

    }