diff --git a/synapse/storage/schema/delta/48/group_unique_indexes.py b/synapse/storage/schema/delta/48/group_unique_indexes.py
new file mode 100644
index 000000000..2233af87d
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+++ b/synapse/storage/schema/delta/48/group_unique_indexes.py
@@ -0,0 +1,57 @@
+# Copyright 2018 New Vector 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.
+
+from synapse.storage.engines import PostgresEngine
+from synapse.storage.prepare_database import get_statements
+
+FIX_INDEXES = """
+-- rebuild indexes as uniques
+DROP INDEX groups_invites_g_idx;
+CREATE UNIQUE INDEX group_invites_g_idx ON group_invites(group_id, user_id);
+DROP INDEX groups_users_g_idx;
+CREATE UNIQUE INDEX group_users_g_idx ON group_users(group_id, user_id);
+
+-- rename other indexes to actually match their table names..
+DROP INDEX groups_users_u_idx;
+CREATE INDEX group_users_u_idx ON group_users(user_id);
+DROP INDEX groups_invites_u_idx;
+CREATE INDEX group_invites_u_idx ON group_invites(user_id);
+DROP INDEX groups_rooms_g_idx;
+CREATE UNIQUE INDEX group_rooms_g_idx ON group_rooms(group_id, room_id);
+DROP INDEX groups_rooms_r_idx;
+CREATE INDEX group_rooms_r_idx ON group_rooms(room_id);
+"""
+
+
+def run_create(cur, database_engine, *args, **kwargs):
+    rowid = "ctid" if isinstance(database_engine, PostgresEngine) else "rowid"
+
+    # remove duplicates from group_users & group_invites tables
+    cur.execute("""
+        DELETE FROM group_users WHERE %s NOT IN (
+           SELECT min(%s) FROM group_users GROUP BY group_id, user_id
+        );
+    """ % (rowid, rowid))
+    cur.execute("""
+        DELETE FROM group_invites WHERE %s NOT IN (
+           SELECT min(%s) FROM group_invites GROUP BY group_id, user_id
+        );
+    """ % (rowid, rowid))
+
+    for statement in get_statements(FIX_INDEXES.splitlines()):
+        cur.execute(statement)
+
+
+def run_upgrade(*args, **kwargs):
+    pass