Sounds like a job for XMLUnit
Example:
public class SomeTest extends XMLTestCase {
@Test
public void test() {
String xml1 = ...
String xml2 = ...
XMLUnit.setIgnoreWhitespace(true); // ignore whitespace differences
// can also compare xml Documents, InputSources, Readers, Diffs
assertXMLEqual(xml1, xml2); // assertXMLEquals comes from XMLTestCase
}
}