diff --git a/hgext/mq.py b/hgext/mq.py
--- a/hgext/mq.py
+++ b/hgext/mq.py
@@ -1504,7 +1504,11 @@ def clone(ui, source, dest=None, **opts)
         if sr.mq.applied:
             qbase = revlog.bin(sr.mq.applied[0].rev)
             if not hg.islocal(dest):
-                destrev = sr.parents(qbase)[0]
+                heads = dict.fromkeys(sr.heads())
+                for h in sr.heads(qbase):
+                    del heads[h]
+                destrev = heads.keys()
+                destrev.append(sr.changelog.parents(qbase)[0])
     ui.note(_('cloning main repo\n'))
     sr, dr = hg.clone(ui, sr, dest,
                       pull=opts['pull'],