diff --git a/lib/notmuch.h b/lib/notmuch.h
index 27b43ff6..73c85a41 100644
--- a/lib/notmuch.h
+++ b/lib/notmuch.h
@@ -500,10 +500,15 @@ typedef enum {
 const char *
 notmuch_query_get_query_string (notmuch_query_t *query);
 
-/* Exclude values for notmuch_query_set_omit_excluded */
+/* Exclude values for notmuch_query_set_omit_excluded. The strange
+ * order is to maintain backward compatibility: the old FALSE/TRUE
+ * options correspond to the new
+ * NOTMUCH_EXCLUDE_FLAG/NOTMUCH_EXCLUDE_TRUE options.
+ */
 typedef enum {
-    NOTMUCH_EXCLUDE_FALSE,
+    NOTMUCH_EXCLUDE_FLAG,
     NOTMUCH_EXCLUDE_TRUE,
+    NOTMUCH_EXCLUDE_FALSE,
     NOTMUCH_EXCLUDE_ALL
 } notmuch_exclude_t;
 
@@ -517,6 +522,15 @@ typedef enum {
  * match in at least one non-excluded message.  Otherwise, if set to ALL,
  * notmuch_query_search_threads will omit excluded messages from all threads.
  *
+ * If set to FALSE or FLAG then both notmuch_query_search_messages and
+ * notmuch_query_search_threads will return all matching
+ * messages/threads regardless of exclude status. If set to FLAG then
+ * the exclude flag will be set for any excluded message that is
+ * returned by notmuch_query_search_messages, and the thread counts
+ * for threads returned by notmuch_query_search_threads will be the
+ * number of non-excluded messages/matches. Otherwise, if set to
+ * FALSE, then the exclude status is completely ignored.
+ *
  * The performance difference when calling
  * notmuch_query_search_messages should be relatively small (and both
  * should be very fast).  However, in some cases,
diff --git a/lib/query.cc b/lib/query.cc
index 1cc768f8..69668a45 100644
--- a/lib/query.cc
+++ b/lib/query.cc
@@ -218,13 +218,15 @@ notmuch_query_search_messages (notmuch_query_t *query)
 	}
 	messages->base.excluded_doc_ids = NULL;
 
-	if (query->exclude_terms) {
+	if ((query->omit_excluded != NOTMUCH_EXCLUDE_FALSE) && (query->exclude_terms)) {
 	    exclude_query = _notmuch_exclude_tags (query, final_query);
 
-	    if (query->omit_excluded != NOTMUCH_EXCLUDE_FALSE)
+	    if (query->omit_excluded == NOTMUCH_EXCLUDE_TRUE ||
+		query->omit_excluded == NOTMUCH_EXCLUDE_ALL)
+	    {
 		final_query = Xapian::Query (Xapian::Query::OP_AND_NOT,
 					     final_query, exclude_query);
-	    else {
+	    } else { /* NOTMUCH_EXCLUDE_FLAG */
 		exclude_query = Xapian::Query (Xapian::Query::OP_AND,
 					   exclude_query, final_query);
 
diff --git a/lib/thread.cc b/lib/thread.cc
index bc078778..4dcf7053 100644
--- a/lib/thread.cc
+++ b/lib/thread.cc
@@ -238,20 +238,22 @@ _thread_add_message (notmuch_thread_t *thread,
     char *clean_author;
     notmuch_bool_t message_excluded = FALSE;
 
-    for (tags = notmuch_message_get_tags (message);
-	 notmuch_tags_valid (tags);
-	 notmuch_tags_move_to_next (tags))
-    {
-	tag = notmuch_tags_get (tags);
-	/* Is message excluded? */
-	for (notmuch_string_node_t *term = exclude_terms->head;
-	     term != NULL;
-	     term = term->next)
+    if (omit_exclude != NOTMUCH_EXCLUDE_FALSE) {
+	for (tags = notmuch_message_get_tags (message);
+	     notmuch_tags_valid (tags);
+	     notmuch_tags_move_to_next (tags))
 	{
-	    /* We ignore initial 'K'. */
-	    if (strcmp(tag, (term->string + 1)) == 0) {
-		message_excluded = TRUE;
-		break;
+	    tag = notmuch_tags_get (tags);
+	    /* Is message excluded? */
+	    for (notmuch_string_node_t *term = exclude_terms->head;
+		 term != NULL;
+		 term = term->next)
+	    {
+		/* We ignore initial 'K'. */
+		if (strcmp(tag, (term->string + 1)) == 0) {
+		    message_excluded = TRUE;
+		    break;
+		}
 	    }
 	}
     }
diff --git a/notmuch-search.c b/notmuch-search.c
index 43232011..a20791a1 100644
--- a/notmuch-search.c
+++ b/notmuch-search.c
@@ -411,7 +411,7 @@ notmuch_search_command (notmuch_config_t *config, int argc, char *argv[])
 	for (i = 0; i < search_exclude_tags_length; i++)
 	    notmuch_query_add_tag_exclude (query, search_exclude_tags[i]);
 	if (exclude == EXCLUDE_FLAG)
-	    notmuch_query_set_omit_excluded (query, NOTMUCH_EXCLUDE_FALSE);
+	    notmuch_query_set_omit_excluded (query, NOTMUCH_EXCLUDE_FLAG);
 	if (exclude == EXCLUDE_ALL)
 	    notmuch_query_set_omit_excluded (query, NOTMUCH_EXCLUDE_ALL);
     }