diff --git a/lib/notmuch-private.h b/lib/notmuch-private.h
index e791bb02..ea836f72 100644
--- a/lib/notmuch-private.h
+++ b/lib/notmuch-private.h
@@ -148,6 +148,8 @@ typedef enum _notmuch_private_status {
 
 typedef struct _notmuch_doc_id_set notmuch_doc_id_set_t;
 
+typedef struct _notmuch_string_list notmuch_string_list_t;
+
 /* database.cc */
 
 /* Lookup a prefix value by name.
@@ -216,6 +218,7 @@ _notmuch_thread_create (void *ctx,
 			notmuch_database_t *notmuch,
 			unsigned int seed_doc_id,
 			notmuch_doc_id_set_t *match_set,
+			notmuch_string_list_t *excluded_terms,
 			notmuch_sort_t sort);
 
 /* message.cc */
@@ -459,11 +462,11 @@ typedef struct _notmuch_string_node {
     struct _notmuch_string_node *next;
 } notmuch_string_node_t;
 
-typedef struct visible _notmuch_string_list {
+struct visible _notmuch_string_list {
     int length;
     notmuch_string_node_t *head;
     notmuch_string_node_t **tail;
-} notmuch_string_list_t;
+};
 
 notmuch_string_list_t *
 _notmuch_string_list_create (const void *ctx);
diff --git a/lib/notmuch.h b/lib/notmuch.h
index f75afaeb..babd2086 100644
--- a/lib/notmuch.h
+++ b/lib/notmuch.h
@@ -672,8 +672,10 @@ notmuch_thread_get_toplevel_messages (notmuch_thread_t *thread);
 /* Get the number of messages in 'thread' that matched the search.
  *
  * This count includes only the messages in this thread that were
- * matched by the search from which the thread was created. Contrast
- * with notmuch_thread_get_total_messages() .
+ * matched by the search from which the thread was created and were
+ * not excluded by any exclude tags passed in with the query (see
+ * notmuch_query_add_tag_exclude). Contrast with
+ * notmuch_thread_get_total_messages() .
  */
 int
 notmuch_thread_get_matched_messages (notmuch_thread_t *thread);
diff --git a/lib/query.cc b/lib/query.cc
index ef2a11f8..ab18fbc6 100644
--- a/lib/query.cc
+++ b/lib/query.cc
@@ -475,6 +475,7 @@ notmuch_threads_get (notmuch_threads_t *threads)
 				   threads->query->notmuch,
 				   doc_id,
 				   &threads->match_set,
+				   threads->query->exclude_terms,
 				   threads->query->sort);
 }
 
diff --git a/lib/thread.cc b/lib/thread.cc
index 0435ee6d..e976d643 100644
--- a/lib/thread.cc
+++ b/lib/thread.cc
@@ -214,7 +214,8 @@ _thread_cleanup_author (notmuch_thread_t *thread,
  */
 static void
 _thread_add_message (notmuch_thread_t *thread,
-		     notmuch_message_t *message)
+		     notmuch_message_t *message,
+		     notmuch_string_list_t *exclude_terms)
 {
     notmuch_tags_t *tags;
     const char *tag;
@@ -262,6 +263,15 @@ _thread_add_message (notmuch_thread_t *thread,
 	 notmuch_tags_move_to_next (tags))
     {
 	tag = notmuch_tags_get (tags);
+	/* Mark excluded messages. */
+	for (notmuch_string_node_t *term = exclude_terms->head; term;
+	     term = term->next) {
+	    /* We ignore initial 'K'. */
+	    if (strcmp(tag, (term->string + 1)) == 0) {
+		notmuch_message_set_flag (message, NOTMUCH_MESSAGE_FLAG_EXCLUDED, TRUE);
+		break;
+	    }
+	}
 	g_hash_table_insert (thread->tags, xstrdup (tag), NULL);
     }
 }
@@ -321,7 +331,8 @@ _thread_add_matched_message (notmuch_thread_t *thread,
 	    _thread_set_subject_from_message (thread, message);
     }
 
-    thread->matched_messages++;
+    if (!notmuch_message_get_flag (message, NOTMUCH_MESSAGE_FLAG_EXCLUDED))
+	thread->matched_messages++;
 
     if (g_hash_table_lookup_extended (thread->message_hash,
 			    notmuch_message_get_message_id (message), NULL,
@@ -392,6 +403,7 @@ _notmuch_thread_create (void *ctx,
 			notmuch_database_t *notmuch,
 			unsigned int seed_doc_id,
 			notmuch_doc_id_set_t *match_set,
+			notmuch_string_list_t *exclude_terms,
 			notmuch_sort_t sort)
 {
     notmuch_thread_t *thread;
@@ -467,7 +479,7 @@ _notmuch_thread_create (void *ctx,
 	if (doc_id == seed_doc_id)
 	    message = seed_message;
 
-	_thread_add_message (thread, message);
+	_thread_add_message (thread, message, exclude_terms);
 
 	if ( _notmuch_doc_id_set_contains (match_set, doc_id)) {
 	    _notmuch_doc_id_set_remove (match_set, doc_id);