diff --git a/hgext/mq.py b/hgext/mq.py
--- a/hgext/mq.py
+++ b/hgext/mq.py
@@ -933,16 +933,20 @@ class queue(object):
             return top, patch
         return None, None
 
-    def checksubstate(self, repo):
+    def checksubstate(self, repo, baserev=None):
         '''return list of subrepos at a different revision than substate.
         Abort if any subrepos have uncommitted changes.'''
         inclsubs = []
         wctx = repo[None]
+        if baserev:
+            bctx = repo[baserev]
+        else:
+            bctx = wctx.parents()[0]
         for s in wctx.substate:
             if wctx.sub(s).dirty(True):
                 raise util.Abort(
                     _("uncommitted changes in subrepository %s") % s)
-            elif wctx.sub(s).dirty():
+            elif s not in bctx.substate or bctx.sub(s).dirty():
                 inclsubs.append(s)
         return inclsubs
 
@@ -1488,13 +1492,14 @@ class queue(object):
                 raise util.Abort(_("cannot refresh immutable revision"),
                                  hint=_('see "hg help phases" for details'))
 
-            inclsubs = self.checksubstate(repo)
+            cparents = repo.changelog.parents(top)
+            patchparent = self.qparents(repo, top)
+
+            inclsubs = self.checksubstate(repo, hex(patchparent))
             if inclsubs:
                 inclsubs.append('.hgsubstate')
                 substatestate = repo.dirstate['.hgsubstate']
 
-            cparents = repo.changelog.parents(top)
-            patchparent = self.qparents(repo, top)
             ph = patchheader(self.join(patchfn), self.plainmode)
             diffopts = self.diffopts({'git': opts.get('git')}, patchfn)
             if msg:
diff --git a/tests/test-mq-subrepo.t b/tests/test-mq-subrepo.t
--- a/tests/test-mq-subrepo.t
+++ b/tests/test-mq-subrepo.t
@@ -441,6 +441,74 @@ both into 'revision' and 'patch file und
   -b6f6e9c41f3dfd374a6d2ed4535c87951cf979cf sub
   +88ac1bef5ed43b689d1d200b59886b675dec474b sub
 
+  $ hg qrefresh -u test -d '0 0'
+  $ cat .hgsubstate
+  88ac1bef5ed43b689d1d200b59886b675dec474b sub
+  $ hg diff -c tip
+  diff -r 44f846335325 -r b3e8c5fa3aaa .hgsubstate
+  --- a/.hgsubstate
+  +++ b/.hgsubstate
+  @@ -1,1 +1,1 @@
+  -b6f6e9c41f3dfd374a6d2ed4535c87951cf979cf sub
+  +88ac1bef5ed43b689d1d200b59886b675dec474b sub
+  $ cat .hg/patches/import-at-qrefresh
+  # HG changeset patch
+  # Date 0 0
+  # User test
+  # Parent 44f846335325209be6be35dc2c9a4be107278c09
+  
+  diff -r 44f846335325 .hgsubstate
+  --- a/.hgsubstate
+  +++ b/.hgsubstate
+  @@ -1,1 +1,1 @@
+  -b6f6e9c41f3dfd374a6d2ed4535c87951cf979cf sub
+  +88ac1bef5ed43b689d1d200b59886b675dec474b sub
+
+  $ hg update -C tip
+  0 files updated, 0 files merged, 0 files removed, 0 files unresolved
+  $ hg qpop -a
+  popping import-at-qrefresh
+  popping import-at-qnew
+  patch queue now empty
+
+  $ hg -R sub update -C 0
+  0 files updated, 0 files merged, 1 files removed, 0 files unresolved
+  $ echo 'sub = sub' > .hgsub
+  $ hg commit -Am '#1 in parent'
+  adding .hgsub
+  $ hg -R sub update -C 1
+  1 files updated, 0 files merged, 0 files removed, 0 files unresolved
+  $ hg commit -Am '#2 in parent (but be rollbacked soon)'
+  $ hg rollback
+  repository tip rolled back to revision 1 (undo commit)
+  working directory now based on revision 1
+  $ hg status
+  M .hgsubstate
+  $ hg qnew -u test -d '0 0' checkstate-at-qnew
+  $ hg -R sub parents --template '{node} sub\n'
+  88ac1bef5ed43b689d1d200b59886b675dec474b sub
+  $ cat .hgsubstate
+  88ac1bef5ed43b689d1d200b59886b675dec474b sub
+  $ hg diff -c tip
+  diff -r 4d91eb2fa1d1 -r 1259c112d884 .hgsubstate
+  --- a/.hgsubstate
+  +++ b/.hgsubstate
+  @@ -1,1 +1,1 @@
+  -b6f6e9c41f3dfd374a6d2ed4535c87951cf979cf sub
+  +88ac1bef5ed43b689d1d200b59886b675dec474b sub
+  $ cat .hg/patches/checkstate-at-qnew
+  # HG changeset patch
+  # Parent 4d91eb2fa1d1b22ec513347b9cd06f6b49d470fa
+  # User test
+  # Date 0 0
+  
+  diff -r 4d91eb2fa1d1 -r 1259c112d884 .hgsubstate
+  --- a/.hgsubstate
+  +++ b/.hgsubstate
+  @@ -1,1 +1,1 @@
+  -b6f6e9c41f3dfd374a6d2ed4535c87951cf979cf sub
+  +88ac1bef5ed43b689d1d200b59886b675dec474b sub
+
   $ cd ..
 
   $ cd ..