diff --git a/synapse/crypto/event_signing.py b/synapse/crypto/event_signing.py
index a115967c0..32d60bd30 100644
--- a/synapse/crypto/event_signing.py
+++ b/synapse/crypto/event_signing.py
@@ -24,15 +24,15 @@ from syutil.crypto.jsonsign import sign_json, verify_signed_json
 import hashlib
 
 
-def hash_event_pdu(pdu, hash_algortithm=hashlib.sha256):
-    hashed = _compute_hash(pdu, hash_algortithm)
+def add_event_pdu_content_hash(pdu, hash_algorithm=hashlib.sha256):
+    hashed = _compute_content_hash(pdu, hash_algorithm)
     pdu.hashes[hashed.name] = encode_base64(hashed.digest())
     return pdu
 
 
-def check_event_pdu_hash(pdu, hash_algorithm=hashlib.sha256):
+def check_event_pdu_content_hash(pdu, hash_algorithm=hashlib.sha256):
     """Check whether the hash for this PDU matches the contents"""
-    computed_hash = _compute_hash(pdu, hash_algortithm)
+    computed_hash = _compute_content_hash(pdu, hash_algortithm)
     if computed_hash.name not in pdu.hashes:
         raise Exception("Algorithm %s not in hashes %s" % (
             computed_hash.name, list(pdu.hashes)
@@ -45,7 +45,7 @@ def check_event_pdu_hash(pdu, hash_algorithm=hashlib.sha256):
     return message_hash_bytes == computed_hash.digest()
 
 
-def _compute_hash(pdu, hash_algorithm):
+def _compute_content_hash(pdu, hash_algorithm):
     pdu_json = pdu.get_dict()
     pdu_json.pop("meta", None)
     pdu_json.pop("signatures", None)
@@ -54,6 +54,15 @@ def _compute_hash(pdu, hash_algorithm):
     return hash_algorithm(pdu_json_bytes)
 
 
+def compute_pdu_event_reference_hash(pdu, hash_algorithm=hashlib.sha256):
+    tmp_pdu = Pdu(**pdu.get_dict())
+    tmp_pdu = prune_pdu(tmp_pdu)
+    pdu_json = tmp_pdu.get_dict()
+    pdu_json_bytes = encode_canonical_json(pdu_json)
+    hashed = hash_algorithm(pdu_json_bytes)
+    return (hashed.name, hashed.digest())
+
+
 def sign_event_pdu(pdu, signature_name, signing_key):
     tmp_pdu = Pdu(**pdu.get_dict())
     tmp_pdu = prune_pdu(tmp_pdu)
diff --git a/synapse/federation/pdu_codec.py b/synapse/federation/pdu_codec.py
index 11fd7264b..7e574f451 100644
--- a/synapse/federation/pdu_codec.py
+++ b/synapse/federation/pdu_codec.py
@@ -14,7 +14,9 @@
 # limitations under the License.
 
 from .units import Pdu
-from synapse.crypto.event_signing import hash_event_pdu, sign_event_pdu
+from synapse.crypto.event_signing import (
+    add_event_pdu_content_hash, sign_event_pdu
+)
 
 import copy
 
@@ -97,5 +99,5 @@ class PduCodec(object):
             kwargs["ts"] = int(self.clock.time_msec())
 
         pdu = Pdu(**kwargs)
-        pdu = hash_event_pdu(pdu)
+        pdu = add_event_pdu_content_hash(pdu)
         return sign_event_pdu(pdu, self.server_name, self.signing_key)
diff --git a/synapse/storage/__init__.py b/synapse/storage/__init__.py
index af05b4793..1738260cc 100644
--- a/synapse/storage/__init__.py
+++ b/synapse/storage/__init__.py
@@ -44,6 +44,8 @@ from .signatures import SignatureStore
 
 from syutil.base64util import decode_base64
 
+from synapse.crypto.event_signing import compute_pdu_event_reference_hash
+
 import json
 import logging
 import os
@@ -165,7 +167,7 @@ class DataStore(RoomMemberStore, RoomStore,
 
         for hash_alg, hash_base64 in pdu.hashes.items():
             hash_bytes = decode_base64(hash_base64)
-            self._store_pdu_hash_txn(
+            self._store_pdu_content_hash_txn(
                 txn, pdu.pdu_id, pdu.origin, hash_alg, hash_bytes,
             )
 
@@ -185,6 +187,11 @@ class DataStore(RoomMemberStore, RoomStore,
                     hash_bytes
                 )
 
+        (ref_alg, ref_hash_bytes) = compute_pdu_event_reference_hash(pdu)
+        self._store_pdu_reference_hash_txn(
+            txn, pdu.pdu_id, pdu.origin, ref_alg, ref_hash_bytes
+        )
+
         if pdu.is_state:
             self._persist_state_txn(txn, pdu.prev_pdus, cols)
         else:
diff --git a/synapse/storage/pdu.py b/synapse/storage/pdu.py
index a423b42db..3a90c382f 100644
--- a/synapse/storage/pdu.py
+++ b/synapse/storage/pdu.py
@@ -69,7 +69,7 @@ class PduStore(SQLBaseStore):
 
             edge_hashes = self._get_prev_pdu_hashes_txn(txn, pdu_id, origin)
 
-            hashes = self._get_pdu_hashes_txn(txn, pdu_id, origin)
+            hashes = self._get_pdu_content_hashes_txn(txn, pdu_id, origin)
             signatures = self._get_pdu_origin_signatures_txn(
                 txn, pdu_id, origin
             )
@@ -317,7 +317,7 @@ class PduStore(SQLBaseStore):
 
         results = []
         for pdu_id, origin, depth in txn.fetchall():
-            hashes = self._get_pdu_hashes_txn(txn, pdu_id, origin)
+            hashes = self._get_pdu_reference_hashes_txn(txn, pdu_id, origin)
             sha256_bytes = hashes["sha256"]
             prev_hashes = {"sha256": encode_base64(sha256_bytes)}
             results.append((pdu_id, origin, prev_hashes, depth))
diff --git a/synapse/storage/schema/signatures.sql b/synapse/storage/schema/signatures.sql
index a72c4dc35..1c45a51be 100644
--- a/synapse/storage/schema/signatures.sql
+++ b/synapse/storage/schema/signatures.sql
@@ -13,7 +13,7 @@
  * limitations under the License.
  */
 
-CREATE TABLE IF NOT EXISTS pdu_hashes (
+CREATE TABLE IF NOT EXISTS pdu_content_hashes (
   pdu_id TEXT,
   origin TEXT,
   algorithm TEXT,
@@ -21,7 +21,21 @@ CREATE TABLE IF NOT EXISTS pdu_hashes (
   CONSTRAINT uniqueness UNIQUE (pdu_id, origin, algorithm)
 );
 
-CREATE INDEX IF NOT EXISTS pdu_hashes_id ON pdu_hashes (pdu_id, origin);
+CREATE INDEX IF NOT EXISTS pdu_content_hashes_id ON pdu_content_hashes (
+    pdu_id, origin
+);
+
+CREATE TABLE IF NOT EXISTS pdu_reference_hashes (
+  pdu_id TEXT,
+  origin TEXT,
+  algorithm TEXT,
+  hash BLOB,
+  CONSTRAINT uniqueness UNIQUE (pdu_id, origin, algorithm)
+);
+
+CREATE INDEX IF NOT EXISTS pdu_reference_hashes_id ON pdu_reference_hashes (
+    pdu_id, origin
+);
 
 CREATE TABLE IF NOT EXISTS pdu_origin_signatures (
   pdu_id TEXT,
diff --git a/synapse/storage/signatures.py b/synapse/storage/signatures.py
index 114710248..85eec7ffb 100644
--- a/synapse/storage/signatures.py
+++ b/synapse/storage/signatures.py
@@ -21,7 +21,7 @@ from twisted.internet import defer
 class SignatureStore(SQLBaseStore):
     """Persistence for PDU signatures and hashes"""
 
-    def _get_pdu_hashes_txn(self, txn, pdu_id, origin):
+    def _get_pdu_content_hashes_txn(self, txn, pdu_id, origin):
         """Get all the hashes for a given PDU.
         Args:
             txn (cursor):
@@ -32,13 +32,14 @@ class SignatureStore(SQLBaseStore):
         """
         query = (
             "SELECT algorithm, hash"
-            " FROM pdu_hashes"
+            " FROM pdu_content_hashes"
             " WHERE pdu_id = ? and origin = ?"
         )
         txn.execute(query, (pdu_id, origin))
         return dict(txn.fetchall())
 
-    def _store_pdu_hash_txn(self, txn, pdu_id, origin, algorithm, hash_bytes):
+    def _store_pdu_content_hash_txn(self, txn, pdu_id, origin, algorithm,
+                                    hash_bytes):
         """Store a hash for a PDU
         Args:
             txn (cursor):
@@ -47,13 +48,48 @@ class SignatureStore(SQLBaseStore):
             algorithm (str): Hashing algorithm.
             hash_bytes (bytes): Hash function output bytes.
         """
-        self._simple_insert_txn(txn, "pdu_hashes", {
+        self._simple_insert_txn(txn, "pdu_content_hashes", {
             "pdu_id": pdu_id,
             "origin": origin,
             "algorithm": algorithm,
             "hash": buffer(hash_bytes),
         })
 
+    def _get_pdu_reference_hashes_txn(self, txn, pdu_id, origin):
+        """Get all the hashes for a given PDU.
+        Args:
+            txn (cursor):
+            pdu_id (str): Id for the PDU.
+            origin (str): origin of the PDU.
+        Returns:
+            A dict of algorithm -> hash.
+        """
+        query = (
+            "SELECT algorithm, hash"
+            " FROM pdu_reference_hashes"
+            " WHERE pdu_id = ? and origin = ?"
+        )
+        txn.execute(query, (pdu_id, origin))
+        return dict(txn.fetchall())
+
+    def _store_pdu_reference_hash_txn(self, txn, pdu_id, origin, algorithm,
+                                      hash_bytes):
+        """Store a hash for a PDU
+        Args:
+            txn (cursor):
+            pdu_id (str): Id for the PDU.
+            origin (str): origin of the PDU.
+            algorithm (str): Hashing algorithm.
+            hash_bytes (bytes): Hash function output bytes.
+        """
+        self._simple_insert_txn(txn, "pdu_reference_hashes", {
+            "pdu_id": pdu_id,
+            "origin": origin,
+            "algorithm": algorithm,
+            "hash": buffer(hash_bytes),
+        })
+
+
     def _get_pdu_origin_signatures_txn(self, txn, pdu_id, origin):
         """Get all the signatures for a given PDU.
         Args: