diff --git a/lib/Doctrine/ORM/Tools/Pagination/CountWalker.php b/lib/Doctrine/ORM/Tools/Pagination/CountWalker.php
index 778dd3072..64914f5a6 100644
--- a/lib/Doctrine/ORM/Tools/Pagination/CountWalker.php
+++ b/lib/Doctrine/ORM/Tools/Pagination/CountWalker.php
@@ -57,7 +57,16 @@ class CountWalker extends TreeWalkerAdapter
                 && $qComp['nestingLevel'] == 0
             ;
             if ($isParent) {
-                $rootComponents[] = array($dqlAlias => $qComp);
+                foreach($AST->fromClause->identificationVariableDeclarations as $identificationVariableDeclaration) {
+                    $isRoot = $identificationVariableDeclaration->rangeVariableDeclaration
+                        && $identificationVariableDeclaration->rangeVariableDeclaration->aliasIdentificationVariable == $dqlAlias
+                        && $identificationVariableDeclaration->rangeVariableDeclaration->isRoot
+                    ;
+                    if ($isRoot) {
+                        $rootComponents[] = array($dqlAlias => $qComp);
+                        break;
+                    }
+                }
             }
         }
         if (count($rootComponents) > 1) {
diff --git a/lib/Doctrine/ORM/Tools/Pagination/WhereInWalker.php b/lib/Doctrine/ORM/Tools/Pagination/WhereInWalker.php
index 27cbc3c2e..460b8a708 100644
--- a/lib/Doctrine/ORM/Tools/Pagination/WhereInWalker.php
+++ b/lib/Doctrine/ORM/Tools/Pagination/WhereInWalker.php
@@ -78,7 +78,16 @@ class WhereInWalker extends TreeWalkerAdapter
                 && $qComp['nestingLevel'] == 0
             ;
             if ($isParent) {
-                $rootComponents[] = array($dqlAlias => $qComp);
+                foreach($AST->fromClause->identificationVariableDeclarations as $identificationVariableDeclaration) {
+                    $isRoot = $identificationVariableDeclaration->rangeVariableDeclaration
+                        && $identificationVariableDeclaration->rangeVariableDeclaration->aliasIdentificationVariable == $dqlAlias
+                        && $identificationVariableDeclaration->rangeVariableDeclaration->isRoot
+                    ;
+                    if ($isRoot) {
+                        $rootComponents[] = array($dqlAlias => $qComp);
+                        break;
+                    }
+                }
             }
         }
         if (count($rootComponents) > 1) {