diff --git a/lib/message.cc b/lib/message.cc
index 225b7e91..adcd07d6 100644
--- a/lib/message.cc
+++ b/lib/message.cc
@@ -254,6 +254,12 @@ _notmuch_message_create_for_message_id (notmuch_database_t *notmuch,
     return message;
 }
 
+unsigned int
+_notmuch_message_get_doc_id (notmuch_message_t *message)
+{
+    return message->doc_id;
+}
+
 const char *
 notmuch_message_get_message_id (notmuch_message_t *message)
 {
diff --git a/lib/notmuch-private.h b/lib/notmuch-private.h
index 592cfb2b..303aeb30 100644
--- a/lib/notmuch-private.h
+++ b/lib/notmuch-private.h
@@ -156,6 +156,8 @@ typedef enum _notmuch_private_status {
      :									\
      (notmuch_status_t) private_status)
 
+typedef struct _notmuch_doc_id_set notmuch_doc_id_set_t;
+
 /* database.cc */
 
 /* Lookup a prefix value by name.
@@ -222,8 +224,8 @@ _notmuch_directory_get_document_id (notmuch_directory_t *directory);
 notmuch_thread_t *
 _notmuch_thread_create (void *ctx,
 			notmuch_database_t *notmuch,
-			const char *thread_id,
-			const char *query_string,
+			unsigned int seed_doc_id,
+			notmuch_doc_id_set_t *match_set,
 			notmuch_sort_t sort);
 
 /* message.cc */
@@ -239,6 +241,9 @@ _notmuch_message_create_for_message_id (notmuch_database_t *notmuch,
 					const char *message_id,
 					notmuch_private_status_t *status);
 
+unsigned int
+_notmuch_message_get_doc_id (notmuch_message_t *message);
+
 const char *
 _notmuch_message_get_in_reply_to (notmuch_message_t *message);
 
@@ -426,6 +431,14 @@ _notmuch_mset_messages_get (notmuch_messages_t *messages);
 void
 _notmuch_mset_messages_move_to_next (notmuch_messages_t *messages);
 
+notmuch_bool_t
+_notmuch_doc_id_set_contains (notmuch_doc_id_set_t *doc_ids,
+                              unsigned int doc_id);
+
+void
+_notmuch_doc_id_set_remove (notmuch_doc_id_set_t *doc_ids,
+                            unsigned int doc_id);
+
 /* message.cc */
 
 void
diff --git a/lib/query.cc b/lib/query.cc
index 7916421e..c7ae4ee7 100644
--- a/lib/query.cc
+++ b/lib/query.cc
@@ -36,13 +36,21 @@ typedef struct _notmuch_mset_messages {
     Xapian::MSetIterator iterator_end;
 } notmuch_mset_messages_t;
 
+struct _notmuch_doc_id_set {
+    unsigned int *bitmap;
+    unsigned int bound;
+};
+
 struct _notmuch_threads {
     notmuch_query_t *query;
-    GHashTable *threads;
-    notmuch_messages_t *messages;
 
-    /* This thread ID is our iterator state. */
-    const char *thread_id;
+    /* The ordered list of doc ids matched by the query. */
+    GArray *doc_ids;
+    /* Our iterator's current position in doc_ids. */
+    unsigned int doc_id_pos;
+    /* The set of matched docid's that have not been assigned to a
+     * thread. Initially, this contains every docid in doc_ids. */
+    notmuch_doc_id_set_t match_set;
 };
 
 notmuch_query_t *
@@ -195,6 +203,19 @@ _notmuch_mset_messages_valid (notmuch_messages_t *messages)
     return (mset_messages->iterator != mset_messages->iterator_end);
 }
 
+static Xapian::docid
+_notmuch_mset_messages_get_doc_id (notmuch_messages_t *messages)
+{
+    notmuch_mset_messages_t *mset_messages;
+
+    mset_messages = (notmuch_mset_messages_t *) messages;
+
+    if (! _notmuch_mset_messages_valid (&mset_messages->base))
+	return 0;
+
+    return *mset_messages->iterator;
+}
+
 notmuch_message_t *
 _notmuch_mset_messages_get (notmuch_messages_t *messages)
 {
@@ -233,6 +254,49 @@ _notmuch_mset_messages_move_to_next (notmuch_messages_t *messages)
     mset_messages->iterator++;
 }
 
+static notmuch_bool_t
+_notmuch_doc_id_set_init (void *ctx,
+			  notmuch_doc_id_set_t *doc_ids,
+			  GArray *arr, unsigned int bound)
+{
+    size_t count = (bound + sizeof (doc_ids->bitmap[0]) - 1) /
+	sizeof (doc_ids->bitmap[0]);
+    unsigned int *bitmap = talloc_zero_array (ctx, unsigned int, count);
+
+    if (bitmap == NULL)
+	return FALSE;
+
+    doc_ids->bitmap = bitmap;
+    doc_ids->bound = bound;
+
+    for (unsigned int i = 0; i < arr->len; i++) {
+	unsigned int doc_id = g_array_index(arr, unsigned int, i);
+	bitmap[doc_id / sizeof (bitmap[0])] |=
+	    1 << (doc_id % sizeof (bitmap[0]));
+    }
+
+    return TRUE;
+}
+
+notmuch_bool_t
+_notmuch_doc_id_set_contains (notmuch_doc_id_set_t *doc_ids,
+			      unsigned int doc_id)
+{
+    if (doc_id >= doc_ids->bound)
+	return FALSE;
+    return (doc_ids->bitmap[doc_id / sizeof (doc_ids->bitmap[0])] &
+	    (1 << (doc_id % sizeof (doc_ids->bitmap[0])))) != 0;
+}
+
+void
+_notmuch_doc_id_set_remove (notmuch_doc_id_set_t *doc_ids,
+                            unsigned int doc_id)
+{
+    if (doc_id < doc_ids->bound)
+	doc_ids->bitmap[doc_id / sizeof (doc_ids->bitmap[0])] &=
+	    ~(1 << (doc_id % sizeof (doc_ids->bitmap[0])));
+}
+
 /* Glib objects force use to use a talloc destructor as well, (but not
  * nearly as ugly as the for messages due to C++ objects). At
  * this point, I'd really like to have some talloc-friendly
@@ -240,7 +304,8 @@ _notmuch_mset_messages_move_to_next (notmuch_messages_t *messages)
 static int
 _notmuch_threads_destructor (notmuch_threads_t *threads)
 {
-    g_hash_table_unref (threads->threads);
+    if (threads->doc_ids)
+	g_array_unref (threads->doc_ids);
 
     return 0;
 }
@@ -249,24 +314,39 @@ notmuch_threads_t *
 notmuch_query_search_threads (notmuch_query_t *query)
 {
     notmuch_threads_t *threads;
+    notmuch_messages_t *messages;
+    Xapian::docid max_doc_id = 0;
 
     threads = talloc (query, notmuch_threads_t);
     if (threads == NULL)
 	return NULL;
+    threads->doc_ids = NULL;
+    talloc_set_destructor (threads, _notmuch_threads_destructor);
 
     threads->query = query;
-    threads->threads = g_hash_table_new_full (g_str_hash, g_str_equal,
-					      free, NULL);
 
-    threads->messages = notmuch_query_search_messages (query);
-    if (threads->messages == NULL) {
+    messages = notmuch_query_search_messages (query);
+    if (messages == NULL) {
 	    talloc_free (threads);
 	    return NULL;
     }
 
-    threads->thread_id = NULL;
+    threads->doc_ids = g_array_new (FALSE, FALSE, sizeof (unsigned int));
+    while (notmuch_messages_valid (messages)) {
+	unsigned int doc_id = _notmuch_mset_messages_get_doc_id (messages);
+	g_array_append_val (threads->doc_ids, doc_id);
+	max_doc_id = MAX (max_doc_id, doc_id);
+	notmuch_messages_move_to_next (messages);
+    }
+    threads->doc_id_pos = 0;
 
-    talloc_set_destructor (threads, _notmuch_threads_destructor);
+    talloc_free (messages);
+
+    if (! _notmuch_doc_id_set_init (threads, &threads->match_set,
+				    threads->doc_ids, max_doc_id + 1)) {
+	talloc_free (threads);
+	return NULL;
+    }
 
     return threads;
 }
@@ -280,51 +360,41 @@ notmuch_query_destroy (notmuch_query_t *query)
 notmuch_bool_t
 notmuch_threads_valid (notmuch_threads_t *threads)
 {
-    notmuch_message_t *message;
+    unsigned int doc_id;
 
-    if (threads->thread_id)
-	return TRUE;
+    while (threads->doc_id_pos < threads->doc_ids->len) {
+	doc_id = g_array_index (threads->doc_ids, unsigned int,
+				threads->doc_id_pos);
+	if (_notmuch_doc_id_set_contains (&threads->match_set, doc_id))
+	    break;
 
-    while (notmuch_messages_valid (threads->messages))
-    {
-	message = notmuch_messages_get (threads->messages);
-
-	threads->thread_id = notmuch_message_get_thread_id (message);
-
-	if (! g_hash_table_lookup_extended (threads->threads,
-					    threads->thread_id,
-					    NULL, NULL))
-	{
-	    g_hash_table_insert (threads->threads,
-				 xstrdup (threads->thread_id), NULL);
-	    notmuch_messages_move_to_next (threads->messages);
-	    return TRUE;
-	}
-
-	notmuch_messages_move_to_next (threads->messages);
+	threads->doc_id_pos++;
     }
 
-    threads->thread_id = NULL;
-    return FALSE;
+    return threads->doc_id_pos < threads->doc_ids->len;
 }
 
 notmuch_thread_t *
 notmuch_threads_get (notmuch_threads_t *threads)
 {
+    unsigned int doc_id;
+
     if (! notmuch_threads_valid (threads))
 	return NULL;
 
+    doc_id = g_array_index (threads->doc_ids, unsigned int,
+			    threads->doc_id_pos);
     return _notmuch_thread_create (threads->query,
 				   threads->query->notmuch,
-				   threads->thread_id,
-				   threads->query->query_string,
+				   doc_id,
+				   &threads->match_set,
 				   threads->query->sort);
 }
 
 void
 notmuch_threads_move_to_next (notmuch_threads_t *threads)
 {
-    threads->thread_id = NULL;
+    threads->doc_id_pos++;
 }
 
 void
diff --git a/lib/thread.cc b/lib/thread.cc
index 31c655b6..b29f2c92 100644
--- a/lib/thread.cc
+++ b/lib/thread.cc
@@ -371,16 +371,17 @@ _resolve_thread_relationships (unused (notmuch_thread_t *thread))
      */
 }
 
-/* Create a new notmuch_thread_t object for the given thread ID,
- * treating any messages matching 'query_string' as "matched".
+/* Create a new notmuch_thread_t object by finding the thread
+ * containing the message with the given doc ID, treating any messages
+ * contained in match_set as "matched".  Remove all messages in the
+ * thread from match_set.
  *
- * Creating the thread will trigger two database searches. The first
- * is for all messages belonging to the thread, (to get the first
- * subject line, the total count of messages, and all authors). The
- * second search is for all messages that are in the thread and that
- * also match the given query_string. This is to allow for a separate
- * count of matched messages, and to allow a viewer to display these
- * messages differently.
+ * Creating the thread will perform a database search to get all
+ * messages belonging to the thread and will get the first subject
+ * line, the total count of messages, and all authors in the thread.
+ * Each message in the thread is checked against match_set to allow
+ * for a separate count of matched messages, and to allow a viewer to
+ * display these messages differently.
  *
  * Here, 'ctx' is talloc context for the resulting thread object.
  *
@@ -389,53 +390,28 @@ _resolve_thread_relationships (unused (notmuch_thread_t *thread))
 notmuch_thread_t *
 _notmuch_thread_create (void *ctx,
 			notmuch_database_t *notmuch,
-			const char *thread_id,
-			const char *query_string,
+			unsigned int seed_doc_id,
+			notmuch_doc_id_set_t *match_set,
 			notmuch_sort_t sort)
 {
     notmuch_thread_t *thread;
+    notmuch_message_t *seed_message;
+    const char *thread_id;
     const char *thread_id_query_string;
     notmuch_query_t *thread_id_query;
 
     notmuch_messages_t *messages;
     notmuch_message_t *message;
-    notmuch_bool_t matched_is_subset_of_thread;
 
+    seed_message = _notmuch_message_create (ctx, notmuch, seed_doc_id, NULL);
+    if (! seed_message)
+	INTERNAL_ERROR ("Thread seed message %u does not exist", seed_doc_id);
+
+    thread_id = notmuch_message_get_thread_id (seed_message);
     thread_id_query_string = talloc_asprintf (ctx, "thread:%s", thread_id);
-    if (unlikely (query_string == NULL))
+    if (unlikely (thread_id_query_string == NULL))
 	return NULL;
 
-    /* Under normal circumstances we need to do two database
-     * queries. One is for the thread itself (thread_id_query_string)
-     * and the second is to determine which messages in that thread
-     * match the original query (matched_query_string).
-     *
-     * But under two circumstances, we use only the
-     * thread_id_query_string:
-     *
-     *	1. If the original query_string *is* just the thread
-     *	   specification.
-     *
-     *  2. If the original query_string matches all messages ("" or
-     *     "*").
-     *
-     * In either of these cases, we can be more efficient by running
-     * just the thread_id query (since we know all messages in the
-     * thread will match the query_string).
-     *
-     * Beyond the performance advantage, in the second case, it's
-     * important to not try to create a concatenated query because our
-     * parser handles "" and "*" as special cases and will not do the
-     * right thing with a query string of "* and thread:<foo>".
-     **/
-    matched_is_subset_of_thread = 1;
-    if (strcmp (query_string, thread_id_query_string) == 0 ||
-	strcmp (query_string, "") == 0 ||
-	strcmp (query_string, "*") == 0)
-    {
-	matched_is_subset_of_thread = 0;
-    }
-
     thread_id_query = notmuch_query_create (notmuch, thread_id_query_string);
     if (unlikely (thread_id_query == NULL))
 	return NULL;
@@ -482,48 +458,25 @@ _notmuch_thread_create (void *ctx,
 	 notmuch_messages_valid (messages);
 	 notmuch_messages_move_to_next (messages))
     {
+	unsigned int doc_id;
+
 	message = notmuch_messages_get (messages);
+	doc_id = _notmuch_message_get_doc_id (message);
+	if (doc_id == seed_doc_id)
+	    message = seed_message;
 
 	_thread_add_message (thread, message);
 
-	if (! matched_is_subset_of_thread)
+	if ( _notmuch_doc_id_set_contains (match_set, doc_id)) {
+	    _notmuch_doc_id_set_remove (match_set, doc_id);
 	    _thread_add_matched_message (thread, message, sort);
+	}
 
 	_notmuch_message_close (message);
     }
 
     notmuch_query_destroy (thread_id_query);
 
-    if (matched_is_subset_of_thread)
-    {
-	const char *matched_query_string;
-	notmuch_query_t *matched_query;
-
-	matched_query_string = talloc_asprintf (ctx, "%s AND (%s)",
-						thread_id_query_string,
-						query_string);
-	if (unlikely (matched_query_string == NULL))
-	    return NULL;
-
-	matched_query = notmuch_query_create (notmuch, matched_query_string);
-	if (unlikely (matched_query == NULL))
-	    return NULL;
-
-	/* As above, we use oldest-first order unconditionally here. */
-	notmuch_query_set_sort (matched_query, NOTMUCH_SORT_OLDEST_FIRST);
-
-	for (messages = notmuch_query_search_messages (matched_query);
-	     notmuch_messages_valid (messages);
-	     notmuch_messages_move_to_next (messages))
-	{
-	    message = notmuch_messages_get (messages);
-	    _thread_add_matched_message (thread, message, sort);
-	    _notmuch_message_close (message);
-	}
-
-	notmuch_query_destroy (matched_query);
-    }
-
     _resolve_thread_authors_string (thread);
 
     _resolve_thread_relationships (thread);