diff --git a/check_model.sh b/check_model.sh
new file mode 100755
index 000000000000..67a2f33720e6
--- /dev/null
+++ b/check_model.sh
@@ -0,0 +1,12 @@
+#!/bin/sh
+
+cd "$(dirname "$0")"
+
+. ./scripts/common_startup_functions.sh
+
+setup_python
+
+python ./scripts/check_model.py "$@"
+
+[ $? -ne 0 ] && exit 1;
+exit 0;
diff --git a/scripts/check_model.py b/scripts/check_model.py
new file mode 100644
index 000000000000..7ca861059d1a
--- /dev/null
+++ b/scripts/check_model.py
@@ -0,0 +1,57 @@
+"""
+Check for db indexes defined in mapping.py but missing in the database.
+Note: pass '-c /path/to/galaxy.yml' to use the database_connection set in galaxy.yml.
+Otherwise the default sqlite database will be used.
+"""
+import json
+import os
+import sys
+from collections import namedtuple
+
+sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, 'lib')))
+
+from sqlalchemy import create_engine, MetaData
+
+from galaxy.model import mapping
+from galaxy.model.orm.scripts import get_config
+
+Index = namedtuple('MissingIndex', 'table column_names')
+
+
+def tuple_from_index(index):
+    columns = tuple([getattr(index.columns, c).name for c in dir(index.columns) if not c.startswith('__')])
+    if len(columns) == 1:
+        columns = columns[0]
+    return Index(index.table.name, columns)
+
+
+def find_missing_indexes():
+
+    def load_indexes(metadata):
+        indexes = {}
+        for t in metadata.tables.values():
+            for index in t.indexes:
+                missing_index = tuple_from_index(index)
+                indexes[missing_index] = index.name
+        return indexes
+
+    # load metadata from mapping.py
+    metadata = mapping.metadata
+    mapping_indexes = load_indexes(metadata)
+
+    # create EMPTY metadata, then load from database
+    db_url = get_config(sys.argv)['db_url']
+    metadata = MetaData(bind=create_engine(db_url))
+    metadata.reflect()
+    indexes_in_db = load_indexes(metadata)
+
+    missing_indexes = set(mapping_indexes.keys()) - set(indexes_in_db.keys())
+    if missing_indexes:
+        return [(mapping_indexes[index], index.table, index.column_names) for index in missing_indexes]
+
+
+if __name__ == '__main__':
+    indexes = find_missing_indexes()
+    if indexes:
+        print(json.dumps(indexes, indent=4))
+        sys.exit(1)