diff --git includes/bootstrap.inc includes/bootstrap.inc
index e931dd7..7d62955 100644
--- includes/bootstrap.inc
+++ includes/bootstrap.inc
@@ -2676,6 +2676,33 @@ function _registry_check_code($type, $name = NULL) {
     return TRUE;
   }
 
+  // Skip classes and interfaces that belong to the database layer.
+  static $database_classes = array(
+    'QueryPlaceholderInterface' => TRUE,
+    'QueryConditionInterface' => TRUE,
+    'DatabaseCondition' => TRUE,
+    'Query' => TRUE,
+    'DeleteQuery' => TRUE,
+    'InsertQuery' => TRUE,
+    'UpdateQuery' => TRUE,
+    'MergeQuery' => TRUE,
+    'TruncateQuery' => TRUE,
+    'QueryAlterableInterface' => TRUE,
+    'SelectQueryInterface' => TRUE,
+    'SelectQuery' => TRUE,
+    'SelectQueryExtender' => TRUE,
+    'DatabaseConnection' => TRUE,
+    'DatabaseLog' => TRUE,
+    'DatabaseTransaction' => TRUE,
+    'DatabaseStatementPrefetch' => TRUE,
+    'DatabaseSchema' => TRUE,
+  );
+  // Those can be optionally suffixed with the engine name, so we only consider
+  // the part of the name before the first underscore.
+  if (($type == 'class' || $type == 'interface') && isset($database_classes[strtok($name, '_')])) {
+    return TRUE;
+  }
+
   if (!isset($lookup_cache)) {
     $lookup_cache = array();
     if ($cache = cache_get('lookup_cache', 'cache_bootstrap')) {
diff --git includes/database/database.inc includes/database/database.inc
index 104d76f..a3d9b0e 100644
--- includes/database/database.inc
+++ includes/database/database.inc
@@ -2123,7 +2123,7 @@ function db_autoload($class) {
       'QueryAlterableInterface',
     ),
     'select.inc' => array('QueryAlterableInterface', 'SelectQueryInterface', 'SelectQuery', 'SelectQueryExtender'),
-    'database.inc' => array('DatabaseConnection'),
+    'database.inc' => array('DatabaseConnection', 'DatabaseTransaction'),
     'log.inc' => array('DatabaseLog'),
     'prefetch.inc' => array('DatabaseStatementPrefetch'),
     'schema.inc' => array('DatabaseSchema'),
diff --git includes/registry.inc includes/registry.inc
index b0faf25..0432c5a 100644
--- includes/registry.inc
+++ includes/registry.inc
@@ -53,6 +53,9 @@ function _registry_update() {
     }
   }
   foreach (file_scan_directory('includes', '/\.inc$/') as $filename => $file) {
+    if (substr($filename, 0, 18) == 'includes/database/') {
+      continue;
+    }
     $files["$filename"] = array('module' => '', 'weight' => 0);
   }