diff --git a/message/lib.php b/message/lib.php
index d79fdc70421..8367e8170a5 100644
--- a/message/lib.php
+++ b/message/lib.php
@@ -220,10 +220,12 @@ function message_count_unread_messages($user1=null, $user2=null) {
     }
 
     if (!empty($user2)) {
-        return $DB->count_records_select('message', "useridto = ? AND useridfrom = ?",
+        return $DB->count_records_select('message', "useridto = ? AND useridfrom = ? AND notification = 0
+            AND timeusertodeleted = 0",
             array($user1->id, $user2->id), "COUNT('id')");
     } else {
-        return $DB->count_records_select('message', "useridto = ?",
+        return $DB->count_records_select('message', "useridto = ? AND notification = 0
+            AND timeusertodeleted = 0",
             array($user1->id), "COUNT('id')");
     }
 }
diff --git a/message/tests/api_test.php b/message/tests/api_test.php
index e0c7c7039c7..35660fc941e 100644
--- a/message/tests/api_test.php
+++ b/message/tests/api_test.php
@@ -73,7 +73,7 @@ class core_message_api_testcase extends core_message_messagelib_testcase {
         $this->send_fake_message($sender2, $recipient);
 
         \core_message\api::mark_all_read_for_user($recipient->id, $sender1->id);
-        $this->assertEquals(message_count_unread_messages($recipient), 6);
+        $this->assertEquals(message_count_unread_messages($recipient), 3);
     }
 
     public function test_mark_all_read_for_user_touser_with_type() {
diff --git a/message/tests/messagelib_test.php b/message/tests/messagelib_test.php
index 351a337015a..bd4a329b080 100644
--- a/message/tests/messagelib_test.php
+++ b/message/tests/messagelib_test.php
@@ -194,6 +194,59 @@ class core_message_messagelib_testcase extends advanced_testcase {
         $this->assertEquals(1, message_count_unread_messages($userto, $userfrom1));
     }
 
+    /**
+     * Test message_count_unread_messages with notifications.
+     */
+    public function test_message_count_unread_messages_with_notifications() {
+        // Create users to send and receive messages.
+        $userfrom1 = $this->getDataGenerator()->create_user();
+        $userfrom2 = $this->getDataGenerator()->create_user();
+        $userto = $this->getDataGenerator()->create_user();
+
+        $this->assertEquals(0, message_count_unread_messages($userto));
+
+        // Send fake messages.
+        $this->send_fake_message($userfrom1, $userto);
+        $this->send_fake_message($userfrom2, $userto);
+
+        // Send fake notifications.
+        $this->send_fake_message($userfrom1, $userto, 'Notification', 1);
+        $this->send_fake_message($userfrom2, $userto, 'Notification', 1);
+
+        // Should only count the messages.
+        $this->assertEquals(2, message_count_unread_messages($userto));
+        $this->assertEquals(1, message_count_unread_messages($userto, $userfrom1));
+    }
+
+    /**
+     * Test message_count_unread_messages with deleted messages.
+     */
+    public function test_message_count_unread_messages_with_deleted_messages() {
+        global $DB;
+
+        // Create users to send and receive messages.
+        $userfrom1 = $this->getDataGenerator()->create_user();
+        $userfrom2 = $this->getDataGenerator()->create_user();
+        $userto = $this->getDataGenerator()->create_user();
+
+        $this->assertEquals(0, message_count_unread_messages($userto));
+
+        // Send fake messages.
+        $messageid = $this->send_fake_message($userfrom1, $userto);
+        $this->send_fake_message($userfrom2, $userto);
+
+        // Send fake notifications.
+        $this->send_fake_message($userfrom1, $userto, 'Notification', 1);
+        $this->send_fake_message($userfrom2, $userto, 'Notification', 1);
+
+        // Delete a message.
+        $message = $DB->get_record('message', array('id' => $messageid));
+        message_delete_message($message, $userto->id);
+
+        // Should only count the messages that weren't deleted by the current user.
+        $this->assertEquals(1, message_count_unread_messages($userto));
+        $this->assertEquals(0, message_count_unread_messages($userto, $userfrom1));
+    }
 
     /**
      * Test message_add_contact.