diff --git a/synapse/storage/prepare_database.py b/synapse/storage/prepare_database.py
index ccaaabcfa0e4..73bbda5b336a 100644
--- a/synapse/storage/prepare_database.py
+++ b/synapse/storage/prepare_database.py
@@ -25,7 +25,7 @@
 
 # Remember to update this number every time a change is made to database
 # schema files, so the users will be informed on server restarts.
-SCHEMA_VERSION = 45
+SCHEMA_VERSION = 46
 
 dir_path = os.path.abspath(os.path.dirname(__file__))
 
diff --git a/synapse/storage/schema/delta/44/thumbnails_index.sql b/synapse/storage/schema/delta/44/thumbnails_index.sql
new file mode 100644
index 000000000000..642fb45af52f
--- /dev/null
+++ b/synapse/storage/schema/delta/44/thumbnails_index.sql
@@ -0,0 +1,25 @@
+/* Copyright 2016 OpenMarket Ltd
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *    http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+CREATE TABLE local_media_repository_thumbnails2 ( media_id TEXT, thumbnail_width INTEGER, thumbnail_height INTEGER, thumbnail_type TEXT, thumbnail_method TEXT, thumbnail_length INTEGER, UNIQUE ( media_id, thumbnail_width, thumbnail_height, thumbnail_type, thumbnail_method ) );
+INSERT INTO local_media_repository_thumbnails2 SELECT * FROM local_media_repository_thumbnails;
+DROP TABLE local_media_repository_thumbnails;
+ALTER TABLE local_media_repository_thumbnails2 RENAME TO local_media_repository_thumbnails;
+CREATE INDEX local_media_repository_thumbnails_media_id ON local_media_repository_thumbnails (media_id);
+
+CREATE TABLE remote_media_cache_thumbnails2 ( media_origin TEXT, media_id TEXT, thumbnail_width INTEGER, thumbnail_height INTEGER, thumbnail_method TEXT, thumbnail_type TEXT, thumbnail_length INTEGER, filesystem_id TEXT, UNIQUE ( media_origin, media_id, thumbnail_width, thumbnail_height, thumbnail_type, thumbnail_method ) );
+INSERT INTO remote_media_cache_thumbnails2 SELECT * FROM remote_media_cache_thumbnails;
+DROP TABLE remote_media_cache_thumbnails;
+ALTER TABLE remote_media_cache_thumbnails2 RENAME TO remote_media_cache_thumbnails;