diff --git a/lib/database.cc b/lib/database.cc
index 91d43298..52ed618b 100644
--- a/lib/database.cc
+++ b/lib/database.cc
@@ -501,8 +501,10 @@ _parse_message_id (void *ctx, const char *message_id, const char **next)
  * 'message_id' in the result (to avoid mass confusion when a single
  * message references itself cyclically---and yes, mail messages are
  * not infrequent in the wild that do this---don't ask me why).
-*/
-static void
+ *
+ * Return the last reference parsed, if it is not equal to message_id.
+ */
+static char *
 parse_references (void *ctx,
 		  const char *message_id,
 		  GHashTable *hash,
@@ -511,7 +513,7 @@ parse_references (void *ctx,
     char *ref;
 
     if (refs == NULL || *refs == '\0')
-	return;
+	return NULL;
 
     while (*refs) {
 	ref = _parse_message_id (ctx, refs, &refs);
@@ -519,6 +521,17 @@ parse_references (void *ctx,
 	if (ref && strcmp (ref, message_id))
 	    g_hash_table_insert (hash, ref, NULL);
     }
+
+    /* The return value of this function is used to add a parent
+     * reference to the database.  We should avoid making a message
+     * its own parent, thus the following check.
+     */
+
+    if (ref && strcmp(ref, message_id)) {
+	return ref;
+    } else {
+	return NULL;
+    }
 }
 
 notmuch_status_t
@@ -1510,28 +1523,33 @@ _notmuch_database_link_message_to_parents (notmuch_database_t *notmuch,
 {
     GHashTable *parents = NULL;
     const char *refs, *in_reply_to, *in_reply_to_message_id;
+    const char *last_ref_message_id, *this_message_id;
     GList *l, *keys = NULL;
     notmuch_status_t ret = NOTMUCH_STATUS_SUCCESS;
 
     parents = g_hash_table_new_full (g_str_hash, g_str_equal,
 				     _my_talloc_free_for_g_hash, NULL);
+    this_message_id = notmuch_message_get_message_id (message);
 
     refs = notmuch_message_file_get_header (message_file, "references");
-    parse_references (message, notmuch_message_get_message_id (message),
-		      parents, refs);
+    last_ref_message_id = parse_references (message,
+					    this_message_id,
+					    parents, refs);
 
     in_reply_to = notmuch_message_file_get_header (message_file, "in-reply-to");
-    parse_references (message, notmuch_message_get_message_id (message),
-		      parents, in_reply_to);
+    in_reply_to_message_id = parse_references (message,
+					       this_message_id,
+					       parents, in_reply_to);
 
-    /* Carefully avoid adding any self-referential in-reply-to term. */
-    in_reply_to_message_id = _parse_message_id (message, in_reply_to, NULL);
-    if (in_reply_to_message_id &&
-	strcmp (in_reply_to_message_id,
-		notmuch_message_get_message_id (message)))
-    {
+    /* For the parent of this message, use the last message ID of the
+     * References header, if available.  If not, fall back to the
+     * first message ID in the In-Reply-To header. */
+    if (last_ref_message_id) {
+        _notmuch_message_add_term (message, "replyto",
+                                   last_ref_message_id);
+    } else if (in_reply_to_message_id) {
 	_notmuch_message_add_term (message, "replyto",
-			     _parse_message_id (message, in_reply_to, NULL));
+			     in_reply_to_message_id);
     }
 
     keys = g_hash_table_get_keys (parents);
diff --git a/test/thread-replies b/test/thread-replies
index 5fc5eedd..eeb70d06 100755
--- a/test/thread-replies
+++ b/test/thread-replies
@@ -12,7 +12,6 @@ test_description='test of proper handling of in-reply-to and references headers'
 . ./test-lib.sh
 
 test_begin_subtest "Use References when In-Reply-To is broken"
-test_subtest_known_broken
 add_message '[id]="foo@one.com"' \
     '[subject]=one'
 add_message '[in-reply-to]="mumble"' \
@@ -47,7 +46,6 @@ expected=`echo "$expected" | notmuch_json_show_sanitize`
 test_expect_equal_json "$output" "$expected"
 
 test_begin_subtest "Prefer References to In-Reply-To"
-test_subtest_known_broken
 add_message '[id]="foo@two.com"' \
     '[subject]=two'
 add_message '[in-reply-to]="<bar@baz.com>"' \
@@ -104,7 +102,6 @@ expected=`echo "$expected" | notmuch_json_show_sanitize`
 test_expect_equal_json "$output" "$expected"
 
 test_begin_subtest "Use last Reference"
-test_subtest_known_broken
 add_message '[id]="foo@four.com"' \
     '[subject]="four"'
 add_message '[id]="bar@four.com"' \