diff --git a/hgext/mq.py b/hgext/mq.py
--- a/hgext/mq.py
+++ b/hgext/mq.py
@@ -793,6 +793,19 @@ class queue(object):
             return top, patch
         return None, None
 
+    def check_substate(self, repo):
+        '''return list of subrepos at a different revision than substate.
+        Abort if any subrepos have uncommitted changes.'''
+        inclsubs = []
+        wctx = repo[None]
+        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():
+                inclsubs.append(s)
+        return inclsubs
+
     def check_localchanges(self, repo, force=False, refresh=True):
         m, a, r, d = repo.status()[:4]
         if (m or a or r or d) and not force:
@@ -826,16 +839,23 @@ class queue(object):
                                  % patchfn)
             else:
                 raise util.Abort(_('patch "%s" already exists') % patchfn)
+
+        inclsubs = self.check_substate(repo)
+        if inclsubs:
+            inclsubs.append('.hgsubstate')
         if opts.get('include') or opts.get('exclude') or pats:
+            if inclsubs:
+                pats = list(pats or []) + inclsubs
             match = cmdutil.match(repo, pats, opts)
             # detect missing files in pats
             def badfn(f, msg):
-                raise util.Abort('%s: %s' % (f, msg))
+                if f != '.hgsubstate': # .hgsubstate is auto-created
+                    raise util.Abort('%s: %s' % (f, msg))
             match.bad = badfn
             m, a, r, d = repo.status(match=match)[:4]
         else:
             m, a, r, d = self.check_localchanges(repo, force=True)
-            match = cmdutil.matchfiles(repo, m + a + r)
+            match = cmdutil.matchfiles(repo, m + a + r + inclsubs)
         if len(repo[None].parents()) > 1:
             raise util.Abort(_('cannot manage merge changesets'))
         commitfiles = m + a + r
@@ -1259,6 +1279,8 @@ class queue(object):
             if repo.changelog.heads(top) != [top]:
                 raise util.Abort(_("cannot refresh a revision with children"))
 
+            inclsubs = self.check_substate(repo)
+
             cparents = repo.changelog.parents(top)
             patchparent = self.qparents(repo, top)
             ph = patchheader(self.join(patchfn), self.plainmode)
@@ -1337,7 +1359,7 @@ class queue(object):
             r = list(dd)
             a = list(aa)
             c = [filter(matchfn, l) for l in (m, a, r)]
-            match = cmdutil.matchfiles(repo, set(c[0] + c[1] + c[2]))
+            match = cmdutil.matchfiles(repo, set(c[0] + c[1] + c[2] + inclsubs))
             chunks = patch.diff(repo, patchparent, match=match,
                                 changes=c, opts=diffopts)
             for chunk in chunks:
diff --git a/mercurial/subrepo.py b/mercurial/subrepo.py
--- a/mercurial/subrepo.py
+++ b/mercurial/subrepo.py
@@ -236,9 +236,10 @@ def subrepo(ctx, path):
 
 class abstractsubrepo(object):
 
-    def dirty(self):
-        """returns true if the dirstate of the subrepo does not match
-        current stored state
+    def dirty(self, ignoreupdate=False):
+        """returns true if the dirstate of the subrepo is dirty or does not
+        match current stored state. If ignoreupdate is true, only check
+        whether the subrepo has uncommitted changes in its dirstate.
         """
         raise NotImplementedError
 
@@ -390,12 +391,13 @@ class hgsubrepo(abstractsubrepo):
             s = subrepo(ctx, subpath)
             s.archive(ui, archiver, os.path.join(prefix, self._path))
 
-    def dirty(self):
+    def dirty(self, ignoreupdate=False):
         r = self._state[1]
-        if r == '':
+        if r == '' and not ignoreupdate: # no state recorded
             return True
         w = self._repo[None]
-        if w.p1() != self._repo[r]: # version checked out change
+        # version checked out changed?
+        if w.p1() != self._repo[r] and not ignoreupdate:
             return True
         return w.dirty() # working directory changed
 
@@ -538,9 +540,10 @@ class svnsubrepo(abstractsubrepo):
                     return True, True
         return bool(changes), False
 
-    def dirty(self):
-        if self._wcrev() == self._state[1] and not self._wcchanged()[0]:
-            return False
+    def dirty(self, ignoreupdate=False):
+        if not self._wcchanged()[0]:
+            if self._wcrev() == self._state[1] and not ignoreupdate:
+                return False
         return True
 
     def commit(self, text, user, date):
diff --git a/tests/test-mq-subrepo.t b/tests/test-mq-subrepo.t
new file mode 100644
--- /dev/null
+++ b/tests/test-mq-subrepo.t
@@ -0,0 +1,342 @@
+  $ echo "[extensions]" >> $HGRCPATH
+  $ echo "mq=" >> $HGRCPATH
+  $ echo "record=" >> $HGRCPATH
+  $ echo "[diff]" >> $HGRCPATH
+  $ echo "nodates=1" >> $HGRCPATH
+
+fn to create new repository w/dirty subrepo, and cd into it
+  $ mkrepo() {
+  >     hg init $1
+  >     cd $1
+  >     hg qinit
+  > }
+
+fn to create dirty subrepo
+  $ mksubrepo() {
+  >     hg init $1
+  >     cd $1
+  >     echo a > a
+  >     hg add
+  >     cd ..
+  > }
+
+  $ testadd() {
+  >     local stdin=`cat`
+  >     mksubrepo sub
+  >     echo sub = sub >> .hgsub
+  >     hg add .hgsub
+  >     echo % abort when adding .hgsub w/dirty subrepo
+  >     hg status -S
+  >     echo '%' $*
+  >     echo "$stdin" | hg $*
+  >     echo [$?]
+  >     hg -R sub ci -m0sub
+  >     echo % update substate when adding .hgsub w/clean updated subrepo
+  >     hg status -S
+  >     echo '%' $*
+  >     echo "$stdin" | hg $*
+  >     hg debugsub
+  > }
+
+  $ testmod() {
+  >     local stdin=`cat`
+  >     mksubrepo sub2
+  >     echo sub2 = sub2 >> .hgsub
+  >     echo % abort when modifying .hgsub w/dirty subrepo
+  >     hg status -S
+  >     echo '%' $*
+  >     echo "$stdin" | hg $*
+  >     echo [$?]
+  >     hg -R sub2 ci -m0sub2
+  >     echo % update substate when modifying .hgsub w/clean updated subrepo
+  >     hg status -S
+  >     echo '%' $*
+  >     echo "$stdin" | hg $*
+  >     hg debugsub
+  > }
+
+  $ testrm1() {
+  >     mksubrepo sub3
+  >     echo sub3 = sub3 >> .hgsub
+  >     hg ci -Aqmsub3
+  >     $EXTRA
+  >     echo b >> sub3/a
+  >     hg rm .hgsub
+  >     echo % update substate when removing .hgsub w/dirty subrepo
+  >     hg status -S
+  >     echo '%' $*
+  >     echo "$stdin" | hg $*
+  >     echo % debugsub should be empty
+  >     hg debugsub
+  > }
+  $ testrm2() {
+  >     mksubrepo sub4
+  >     echo sub4 = sub4 >> .hgsub
+  >     hg ci -Aqmsub4
+  >     $EXTRA
+  >     hg rm .hgsub
+  >     echo % update substate when removing .hgsub w/clean updated subrepo
+  >     hg status -S
+  >     echo '%' $*
+  >     echo "$stdin" | hg $*
+  >     echo % debugsub should be empty
+  >     hg debugsub
+  > }
+
+
+handle subrepos safely on qnew
+
+  $ mkrepo repo-2499-qnew
+  $ testadd qnew -m0 0.diff
+  adding a
+  % abort when adding .hgsub w/dirty subrepo
+  A .hgsub
+  A sub/a
+  % qnew -m0 0.diff
+  abort: uncommitted changes in subrepository sub
+  [255]
+  % update substate when adding .hgsub w/clean updated subrepo
+  A .hgsub
+  % qnew -m0 0.diff
+  committing subrepository sub
+  path sub
+   source   sub
+   revision b2fdb12cd82b021c3b7053d67802e77b6eeaee31
+
+  $ testmod qnew -m1 1.diff
+  adding a
+  % abort when modifying .hgsub w/dirty subrepo
+  M .hgsub
+  A sub2/a
+  % qnew -m1 1.diff
+  abort: uncommitted changes in subrepository sub2
+  [255]
+  % update substate when modifying .hgsub w/clean updated subrepo
+  M .hgsub
+  % qnew -m1 1.diff
+  committing subrepository sub2
+  path sub
+   source   sub
+   revision b2fdb12cd82b021c3b7053d67802e77b6eeaee31
+  path sub2
+   source   sub2
+   revision 1f94c7611cc6b74f5a17b16121a1170d44776845
+
+  $ hg qpop -qa
+  patch queue now empty
+  $ testrm1 qnew -m2 2.diff
+  adding a
+  % update substate when removing .hgsub w/dirty subrepo
+  M sub3/a
+  R .hgsub
+  % qnew -m2 2.diff
+  % debugsub should be empty
+
+  $ hg qpop -qa
+  patch queue now empty
+  $ testrm2 qnew -m3 3.diff
+  adding a
+  % update substate when removing .hgsub w/clean updated subrepo
+  R .hgsub
+  % qnew -m3 3.diff
+  % debugsub should be empty
+
+  $ cd ..
+
+
+handle subrepos safely on qrefresh
+
+  $ mkrepo repo-2499-qrefresh
+  $ hg qnew -m0 0.diff
+  $ testadd qrefresh
+  adding a
+  % abort when adding .hgsub w/dirty subrepo
+  A .hgsub
+  A sub/a
+  % qrefresh
+  abort: uncommitted changes in subrepository sub
+  [255]
+  % update substate when adding .hgsub w/clean updated subrepo
+  A .hgsub
+  % qrefresh
+  committing subrepository sub
+  path sub
+   source   sub
+   revision b2fdb12cd82b021c3b7053d67802e77b6eeaee31
+
+  $ hg qnew -m1 1.diff
+  $ testmod qrefresh
+  adding a
+  % abort when modifying .hgsub w/dirty subrepo
+  M .hgsub
+  A sub2/a
+  % qrefresh
+  abort: uncommitted changes in subrepository sub2
+  [255]
+  % update substate when modifying .hgsub w/clean updated subrepo
+  M .hgsub
+  % qrefresh
+  committing subrepository sub2
+  path sub
+   source   sub
+   revision b2fdb12cd82b021c3b7053d67802e77b6eeaee31
+  path sub2
+   source   sub2
+   revision 1f94c7611cc6b74f5a17b16121a1170d44776845
+
+  $ hg qpop -qa
+  patch queue now empty
+  $ EXTRA='hg qnew -m2 2.diff' testrm1 qrefresh
+  adding a
+  % update substate when removing .hgsub w/dirty subrepo
+  M sub3/a
+  R .hgsub
+  % qrefresh
+  % debugsub should be empty
+
+  $ hg qpop -qa
+  patch queue now empty
+  $ EXTRA='hg qnew -m3 3.diff' testrm2 qrefresh
+  adding a
+  % update substate when removing .hgsub w/clean updated subrepo
+  R .hgsub
+  % qrefresh
+  % debugsub should be empty
+
+  $ cd ..
+
+
+handle subrepos safely on qpush/qpop
+
+  $ mkrepo repo-2499-qpush
+  $ mksubrepo sub
+  adding a
+  $ hg -R sub ci -m0sub
+  $ echo sub = sub > .hgsub
+  $ hg add .hgsub
+  $ hg qnew -m0 0.diff
+  committing subrepository sub
+  $ hg debugsub
+  path sub
+   source   sub
+   revision b2fdb12cd82b021c3b7053d67802e77b6eeaee31
+
+qpop
+  $ hg qpop
+  popping 0.diff
+  patch queue now empty
+  $ hg status -AS
+  $ hg debugsub
+
+qpush
+  $ hg qpush
+  applying 0.diff
+  now at: 0.diff
+  $ hg status -AS
+  C .hgsub
+  C .hgsubstate
+  C sub/a
+  $ hg debugsub
+  path sub
+   source   sub
+   revision b2fdb12cd82b021c3b7053d67802e77b6eeaee31
+
+  $ cd ..
+
+
+handle subrepos safely on qrecord
+
+  $ mkrepo repo-2499-qrecord
+  $ testadd qrecord --config ui.interactive=1 -m0 0.diff <<EOF
+  > y
+  > y
+  > EOF
+  adding a
+  % abort when adding .hgsub w/dirty subrepo
+  A .hgsub
+  A sub/a
+  % qrecord --config ui.interactive=1 -m0 0.diff
+  diff --git a/.hgsub b/.hgsub
+  new file mode 100644
+  examine changes to '.hgsub'? [Ynsfdaq?] 
+  abort: uncommitted changes in subrepository sub
+  [255]
+  % update substate when adding .hgsub w/clean updated subrepo
+  A .hgsub
+  % qrecord --config ui.interactive=1 -m0 0.diff
+  diff --git a/.hgsub b/.hgsub
+  new file mode 100644
+  examine changes to '.hgsub'? [Ynsfdaq?] 
+  committing subrepository sub
+  path sub
+   source   sub
+   revision b2fdb12cd82b021c3b7053d67802e77b6eeaee31
+
+  $ testmod qrecord --config ui.interactive=1 -m1 1.diff <<EOF
+  > y
+  > y
+  > EOF
+  adding a
+  % abort when modifying .hgsub w/dirty subrepo
+  M .hgsub
+  A sub2/a
+  % qrecord --config ui.interactive=1 -m1 1.diff
+  diff --git a/.hgsub b/.hgsub
+  1 hunks, 1 lines changed
+  examine changes to '.hgsub'? [Ynsfdaq?] 
+  @@ -1,1 +1,2 @@
+   sub = sub
+  +sub2 = sub2
+  record this change to '.hgsub'? [Ynsfdaq?] 
+  abort: uncommitted changes in subrepository sub2
+  [255]
+  % update substate when modifying .hgsub w/clean updated subrepo
+  M .hgsub
+  % qrecord --config ui.interactive=1 -m1 1.diff
+  diff --git a/.hgsub b/.hgsub
+  1 hunks, 1 lines changed
+  examine changes to '.hgsub'? [Ynsfdaq?] 
+  @@ -1,1 +1,2 @@
+   sub = sub
+  +sub2 = sub2
+  record this change to '.hgsub'? [Ynsfdaq?] 
+  committing subrepository sub2
+  path sub
+   source   sub
+   revision b2fdb12cd82b021c3b7053d67802e77b6eeaee31
+  path sub2
+   source   sub2
+   revision 1f94c7611cc6b74f5a17b16121a1170d44776845
+
+  $ hg qpop -qa
+  patch queue now empty
+  $ EXTRA= testrm1 qrecord --config ui.interactive=1 -m2 2.diff <<EOF
+  > y
+  > y
+  > EOF
+  adding a
+  % update substate when removing .hgsub w/dirty subrepo
+  M sub3/a
+  R .hgsub
+  % qrecord --config ui.interactive=1 -m2 2.diff
+  diff --git a/.hgsub b/.hgsub
+  deleted file mode 100644
+  examine changes to '.hgsub'? [Ynsfdaq?] 
+  % debugsub should be empty
+
+  $ hg qpop -qa
+  patch queue now empty
+  $ EXTRA= testrm2 qrecord --config ui.interactive=1 -m3 3.diff <<EOF
+  > y
+  > y
+  > EOF
+  adding a
+  % update substate when removing .hgsub w/clean updated subrepo
+  R .hgsub
+  % qrecord --config ui.interactive=1 -m3 3.diff
+  diff --git a/.hgsub b/.hgsub
+  deleted file mode 100644
+  examine changes to '.hgsub'? [Ynsfdaq?] 
+  % debugsub should be empty
+
+  $ cd ..