diff --git a/hgext/mq.py b/hgext/mq.py
--- a/hgext/mq.py
+++ b/hgext/mq.py
@@ -1035,7 +1035,6 @@ class queue(object):
             self.checkpatchname(patchfn)
         inclsubs = checksubstate(repo)
         if inclsubs:
-            inclsubs.append('.hgsubstate')
             substatestate = repo.dirstate['.hgsubstate']
         if opts.get('include') or opts.get('exclude') or pats:
             match = scmutil.match(repo[None], pats, opts)
@@ -1045,14 +1044,14 @@ class queue(object):
                     raise util.Abort('%s: %s' % (f, msg))
             match.bad = badfn
             changes = repo.status(match=match)
-            m, a, r, d = changes[:4]
         else:
             changes = self.checklocalchanges(repo, force=True)
-            m, a, r, d = changes
-        match = scmutil.matchfiles(repo, m + a + r + inclsubs)
+        commitfiles = list(inclsubs)
+        for files in changes[:3]:
+            commitfiles.extend([f for f in files if f != '.hgsubstate'])
+        match = scmutil.matchfiles(repo, commitfiles)
         if len(repo[None].parents()) > 1:
             raise util.Abort(_('cannot manage merge changesets'))
-        commitfiles = m + a + r
         self.checktoppatch(repo)
         insert = self.fullseriesend()
         wlock = repo.wlock()
@@ -1492,7 +1491,6 @@ class queue(object):
 
             inclsubs = checksubstate(repo, hex(patchparent))
             if inclsubs:
-                inclsubs.append('.hgsubstate')
                 substatestate = repo.dirstate['.hgsubstate']
 
             ph = patchheader(self.join(patchfn), self.plainmode)
@@ -1579,7 +1577,7 @@ class queue(object):
 
             files = set(inclsubs)
             for x in refreshchanges:
-                files.update(x)
+                files.update([f for f in x if f != '.hgsubstate'])
             match = scmutil.matchfiles(repo, files)
 
             bmlist = repo[top].bookmarks()
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
@@ -407,12 +407,12 @@ both into 'revision' and 'patch file und
   $ cat .hgsubstate
   b6f6e9c41f3dfd374a6d2ed4535c87951cf979cf sub
   $ hg diff -c tip
-  diff -r f499373e340c -r b20ffac88564 .hgsub
+  diff -r f499373e340c -r f69e96d86e75 .hgsub
   --- /dev/null
   +++ b/.hgsub
   @@ -0,0 +1,1 @@
   +sub = sub
-  diff -r f499373e340c -r b20ffac88564 .hgsubstate
+  diff -r f499373e340c -r f69e96d86e75 .hgsubstate
   --- /dev/null
   +++ b/.hgsubstate
   @@ -0,0 +1,1 @@
@@ -423,16 +423,34 @@ both into 'revision' and 'patch file und
   # User test
   # Date 0 0
   
-  diff -r f499373e340c -r b20ffac88564 .hgsub
+  diff -r f499373e340c -r f69e96d86e75 .hgsub
   --- /dev/null
   +++ b/.hgsub
   @@ -0,0 +1,1 @@
   +sub = sub
-  diff -r f499373e340c -r b20ffac88564 .hgsubstate
+  diff -r f499373e340c -r f69e96d86e75 .hgsubstate
   --- /dev/null
   +++ b/.hgsubstate
   @@ -0,0 +1,1 @@
   +b6f6e9c41f3dfd374a6d2ed4535c87951cf979cf sub
+  $ hg parents --template '{node}\n'
+  f69e96d86e75a6d4fd88285dc9697acb23951041
+
+check also whether qnew not including ".hgsubstate" explicitly causes
+as same result (in node hash) as one including it.
+
+  $ hg qpop -a -q
+  patch queue now empty
+  $ hg qdelete import-at-qnew
+  $ echo 'sub = sub' > .hgsub
+  $ hg add .hgsub
+  $ rm -f .hgsubstate
+  $ hg qnew -u test -d '0 0' import-at-qnew
+  $ hg parents --template '{node}\n'
+  f69e96d86e75a6d4fd88285dc9697acb23951041
+
+check whether qrefresh imports updated .hgsubstate correctly
+
   $ hg qpop
   popping import-at-qnew
   patch queue now empty
@@ -537,6 +555,31 @@ both into 'revision' and 'patch file und
   -b6f6e9c41f3dfd374a6d2ed4535c87951cf979cf sub
   +88ac1bef5ed43b689d1d200b59886b675dec474b sub
 
+check whether qrefresh not including ".hgsubstate" explicitly causes
+as same result (in node hash) as one including it.
+
+  $ hg update -C -q 0
+  $ hg qpop -a -q
+  patch queue now empty
+  $ hg qnew -u test -d '0 0' add-hgsub-at-qrefresh
+  $ echo 'sub = sub' > .hgsub
+  $ echo > .hgsubstate
+  $ hg add .hgsub .hgsubstate
+  $ hg qrefresh -u test -d '0 0'
+  $ hg parents --template '{node}\n'
+  7c48c35501aae6770ed9c2517014628615821a8e
+
+  $ hg qpop -a -q
+  patch queue now empty
+  $ hg qdelete add-hgsub-at-qrefresh
+  $ hg qnew -u test -d '0 0' add-hgsub-at-qrefresh
+  $ echo 'sub = sub' > .hgsub
+  $ hg add .hgsub
+  $ rm -f .hgsubstate
+  $ hg qrefresh -u test -d '0 0'
+  $ hg parents --template '{node}\n'
+  7c48c35501aae6770ed9c2517014628615821a8e
+
   $ cd ..
 
   $ cd ..