diff --git a/lib/Doctrine/ORM/Tools/Pagination/CountOutputWalker.php b/lib/Doctrine/ORM/Tools/Pagination/CountOutputWalker.php
index a65c73328..e44be6c57 100644
--- a/lib/Doctrine/ORM/Tools/Pagination/CountOutputWalker.php
+++ b/lib/Doctrine/ORM/Tools/Pagination/CountOutputWalker.php
@@ -96,7 +96,8 @@ class CountOutputWalker extends SqlWalker
             throw new \RuntimeException("Cannot count query which selects two FROM components, cannot make distinction");
         }
 
-        $rootAlias      = $from[0]->rangeVariableDeclaration->aliasIdentificationVariable;
+        $fromRoot       = reset($from);
+        $rootAlias      = $fromRoot->rangeVariableDeclaration->aliasIdentificationVariable;
         $rootClass      = $this->queryComponents[$rootAlias]['metadata'];
         $rootIdentifier = $rootClass->identifier;
 
diff --git a/lib/Doctrine/ORM/Tools/Pagination/CountWalker.php b/lib/Doctrine/ORM/Tools/Pagination/CountWalker.php
index 778dd3072..ff0c6b363 100644
--- a/lib/Doctrine/ORM/Tools/Pagination/CountWalker.php
+++ b/lib/Doctrine/ORM/Tools/Pagination/CountWalker.php
@@ -50,31 +50,26 @@ class CountWalker extends TreeWalkerAdapter
             throw new \RuntimeException('Cannot count query that uses a HAVING clause. Use the output walkers for pagination');
         }
 
-        $rootComponents = array();
-        foreach ($this->_getQueryComponents() as $dqlAlias => $qComp) {
-            $isParent = array_key_exists('parent', $qComp)
-                && $qComp['parent'] === null
-                && $qComp['nestingLevel'] == 0
-            ;
-            if ($isParent) {
-                $rootComponents[] = array($dqlAlias => $qComp);
-            }
-        }
-        if (count($rootComponents) > 1) {
+        $queryComponents = $this->_getQueryComponents();
+        // Get the root entity and alias from the AST fromClause
+        $from = $AST->fromClause->identificationVariableDeclarations;
+        
+        if (count($from) > 1) {
             throw new \RuntimeException("Cannot count query which selects two FROM components, cannot make distinction");
         }
-        $root                = reset($rootComponents);
-        $parentName          = key($root);
-        $parent              = current($root);
-        $identifierFieldName = $parent['metadata']->getSingleIdentifierFieldName();
+       
+        $fromRoot            = reset($from);
+        $rootAlias           = $fromRoot->rangeVariableDeclaration->aliasIdentificationVariable;
+        $rootClass           = $queryComponents[$rootAlias]['metadata'];
+        $identifierFieldName = $rootClass->getSingleIdentifierFieldName();
 
         $pathType = PathExpression::TYPE_STATE_FIELD;
-        if (isset($parent['metadata']->associationMappings[$identifierFieldName])) {
+        if (isset($rootClass->associationMappings[$identifierFieldName])) {
             $pathType = PathExpression::TYPE_SINGLE_VALUED_ASSOCIATION;
         }
 
         $pathExpression = new PathExpression(
-            PathExpression::TYPE_STATE_FIELD | PathExpression::TYPE_SINGLE_VALUED_ASSOCIATION, $parentName,
+            PathExpression::TYPE_STATE_FIELD | PathExpression::TYPE_SINGLE_VALUED_ASSOCIATION, $rootAlias,
             $identifierFieldName
         );
         $pathExpression->type = $pathType;
diff --git a/lib/Doctrine/ORM/Tools/Pagination/LimitSubqueryOutputWalker.php b/lib/Doctrine/ORM/Tools/Pagination/LimitSubqueryOutputWalker.php
index 1b32fc97c..45a6ce78b 100644
--- a/lib/Doctrine/ORM/Tools/Pagination/LimitSubqueryOutputWalker.php
+++ b/lib/Doctrine/ORM/Tools/Pagination/LimitSubqueryOutputWalker.php
@@ -122,7 +122,8 @@ class LimitSubqueryOutputWalker extends SqlWalker
             throw new \RuntimeException("Cannot count query which selects two FROM components, cannot make distinction");
         }
 
-        $rootAlias      = $from[0]->rangeVariableDeclaration->aliasIdentificationVariable;
+        $fromRoot       = reset($from);
+        $rootAlias      = $fromRoot->rangeVariableDeclaration->aliasIdentificationVariable;
         $rootClass      = $this->queryComponents[$rootAlias]['metadata'];
         $rootIdentifier = $rootClass->identifier;
 
diff --git a/lib/Doctrine/ORM/Tools/Pagination/LimitSubqueryWalker.php b/lib/Doctrine/ORM/Tools/Pagination/LimitSubqueryWalker.php
index 2cf5e527f..c88191153 100644
--- a/lib/Doctrine/ORM/Tools/Pagination/LimitSubqueryWalker.php
+++ b/lib/Doctrine/ORM/Tools/Pagination/LimitSubqueryWalker.php
@@ -60,37 +60,36 @@ class LimitSubqueryWalker extends TreeWalkerAdapter
      */
     public function walkSelectStatement(SelectStatement $AST)
     {
-        $parent = null;
-        $parentName = null;
+        $queryComponents = $this->_getQueryComponents();
+        // Get the root entity and alias from the AST fromClause
+        $from      = $AST->fromClause->identificationVariableDeclarations;
+        $fromRoot  = reset($from);
+        $rootAlias = $fromRoot->rangeVariableDeclaration->aliasIdentificationVariable;
+        $rootClass = $queryComponents[$rootAlias]['metadata'];
         $selectExpressions = array();
 
-        foreach ($this->_getQueryComponents() as $dqlAlias => $qComp) {
+        foreach ($queryComponents as $dqlAlias => $qComp) {
             // Preserve mixed data in query for ordering.
             if (isset($qComp['resultVariable'])) {
                 $selectExpressions[] = new SelectExpression($qComp['resultVariable'], $dqlAlias);
                 continue;
             }
-
-            if ($qComp['parent'] === null && $qComp['nestingLevel'] == 0) {
-                $parent = $qComp;
-                $parentName = $dqlAlias;
-                continue;
-            }
         }
-
-        $identifier = $parent['metadata']->getSingleIdentifierFieldName();
-        if (isset($parent['metadata']->associationMappings[$identifier])) {
+        
+        $identifier = $rootClass->getSingleIdentifierFieldName();
+        
+        if (isset($rootClass->associationMappings[$identifier])) {
             throw new \RuntimeException("Paginating an entity with foreign key as identifier only works when using the Output Walkers. Call Paginator#setUseOutputWalkers(true) before iterating the paginator.");
         }
 
         $this->_getQuery()->setHint(
             self::IDENTIFIER_TYPE,
-            Type::getType($parent['metadata']->getTypeOfField($identifier))
+            Type::getType($rootClass->getTypeOfField($identifier))
         );
 
         $pathExpression = new PathExpression(
             PathExpression::TYPE_STATE_FIELD | PathExpression::TYPE_SINGLE_VALUED_ASSOCIATION,
-            $parentName,
+            $rootAlias,
             $identifier
         );
         $pathExpression->type = PathExpression::TYPE_STATE_FIELD;
diff --git a/lib/Doctrine/ORM/Tools/Pagination/WhereInWalker.php b/lib/Doctrine/ORM/Tools/Pagination/WhereInWalker.php
index 27cbc3c2e..9f42a1eea 100644
--- a/lib/Doctrine/ORM/Tools/Pagination/WhereInWalker.php
+++ b/lib/Doctrine/ORM/Tools/Pagination/WhereInWalker.php
@@ -71,30 +71,25 @@ class WhereInWalker extends TreeWalkerAdapter
      */
     public function walkSelectStatement(SelectStatement $AST)
     {
-        $rootComponents = array();
-        foreach ($this->_getQueryComponents() as $dqlAlias => $qComp) {
-            $isParent = array_key_exists('parent', $qComp)
-                && $qComp['parent'] === null
-                && $qComp['nestingLevel'] == 0
-            ;
-            if ($isParent) {
-                $rootComponents[] = array($dqlAlias => $qComp);
-            }
-        }
-        if (count($rootComponents) > 1) {
+        $queryComponents = $this->_getQueryComponents();
+        // Get the root entity and alias from the AST fromClause
+        $from = $AST->fromClause->identificationVariableDeclarations;
+        
+        if (count($from) > 1) {
             throw new \RuntimeException("Cannot count query which selects two FROM components, cannot make distinction");
         }
-        $root                = reset($rootComponents);
-        $parentName          = key($root);
-        $parent              = current($root);
-        $identifierFieldName = $parent['metadata']->getSingleIdentifierFieldName();
+       
+        $fromRoot            = reset($from);
+        $rootAlias           = $fromRoot->rangeVariableDeclaration->aliasIdentificationVariable;
+        $rootClass           = $queryComponents[$rootAlias]['metadata'];
+        $identifierFieldName = $rootClass->getSingleIdentifierFieldName();
 
         $pathType = PathExpression::TYPE_STATE_FIELD;
-        if (isset($parent['metadata']->associationMappings[$identifierFieldName])) {
+        if (isset($rootClass->associationMappings[$identifierFieldName])) {
             $pathType = PathExpression::TYPE_SINGLE_VALUED_ASSOCIATION;
         }
 
-        $pathExpression       = new PathExpression(PathExpression::TYPE_STATE_FIELD | PathExpression::TYPE_SINGLE_VALUED_ASSOCIATION, $parentName, $identifierFieldName);
+        $pathExpression       = new PathExpression(PathExpression::TYPE_STATE_FIELD | PathExpression::TYPE_SINGLE_VALUED_ASSOCIATION, $rootAlias, $identifierFieldName);
         $pathExpression->type = $pathType;
 
         $count = $this->_getQuery()->getHint(self::HINT_PAGINATOR_ID_COUNT);
diff --git a/tests/Doctrine/Tests/ORM/Tools/Pagination/CountWalkerTest.php b/tests/Doctrine/Tests/ORM/Tools/Pagination/CountWalkerTest.php
index 4ef4d1630..e44248926 100644
--- a/tests/Doctrine/Tests/ORM/Tools/Pagination/CountWalkerTest.php
+++ b/tests/Doctrine/Tests/ORM/Tools/Pagination/CountWalkerTest.php
@@ -90,5 +90,21 @@ class CountWalkerTest extends PaginationTestCase
 
         $query->getSql();
     }
+    
+    /**
+     * Arbitrary Join 
+     */
+    public function testCountQueryWithArbitraryJoin()
+    {
+        $query = $this->entityManager->createQuery(
+            'SELECT p FROM Doctrine\Tests\ORM\Tools\Pagination\BlogPost p LEFT JOIN Doctrine\Tests\ORM\Tools\Pagination\Category c WITH p.category = c');
+        $query->setHint(Query::HINT_CUSTOM_TREE_WALKERS, array('Doctrine\ORM\Tools\Pagination\CountWalker'));
+        $query->setHint(CountWalker::HINT_DISTINCT, true);
+        $query->setFirstResult(null)->setMaxResults(null);
+
+        $this->assertEquals(
+            "SELECT count(DISTINCT b0_.id) AS sclr_0 FROM BlogPost b0_ LEFT JOIN Category c1_ ON (b0_.category_id = c1_.id)", $query->getSql()
+        );
+    }
 }
 
diff --git a/tests/Doctrine/Tests/ORM/Tools/Pagination/LimitSubqueryWalkerTest.php b/tests/Doctrine/Tests/ORM/Tools/Pagination/LimitSubqueryWalkerTest.php
index 1bb2b6463..597ec1350 100644
--- a/tests/Doctrine/Tests/ORM/Tools/Pagination/LimitSubqueryWalkerTest.php
+++ b/tests/Doctrine/Tests/ORM/Tools/Pagination/LimitSubqueryWalkerTest.php
@@ -67,5 +67,36 @@ class LimitSubqueryWalkerTest extends PaginationTestCase
             $limitQuery->getSql()
         );
     }
+    
+    /**
+     * Arbitrary Join 
+     */     
+     public function testLimitSubqueryWithArbitraryJoin()
+    {
+        $dql        = 'SELECT p, c FROM Doctrine\Tests\ORM\Tools\Pagination\MyBlogPost p JOIN Doctrine\Tests\ORM\Tools\Pagination\Category c WITH p.category = c';
+        $query      = $this->entityManager->createQuery($dql);
+        $limitQuery = clone $query;
+        
+        $limitQuery->setHint(Query::HINT_CUSTOM_TREE_WALKERS, array('Doctrine\ORM\Tools\Pagination\LimitSubqueryWalker'));
+
+        $this->assertEquals(
+            "SELECT DISTINCT m0_.id AS id_0 FROM MyBlogPost m0_ INNER JOIN Category c1_ ON (m0_.category_id = c1_.id)", 
+            $limitQuery->getSql()
+        );
+    }
+
+    public function testLimitSubqueryWithSortWithArbitraryJoin()
+    {
+        $dql        = 'SELECT p, c FROM Doctrine\Tests\ORM\Tools\Pagination\MyBlogPost p JOIN Doctrine\Tests\ORM\Tools\Pagination\Category c WITH p.category = c ORDER BY p.title';
+        $query      = $this->entityManager->createQuery($dql);
+        $limitQuery = clone $query;
+        
+        $limitQuery->setHint(Query::HINT_CUSTOM_TREE_WALKERS, array('Doctrine\ORM\Tools\Pagination\LimitSubqueryWalker'));
+
+        $this->assertEquals(
+            "SELECT DISTINCT m0_.id AS id_0, m0_.title AS title_1 FROM MyBlogPost m0_ INNER JOIN Category c1_ ON (m0_.category_id = c1_.id) ORDER BY m0_.title ASC", 
+            $limitQuery->getSql()
+        );
+    }
 }
 
diff --git a/tests/Doctrine/Tests/ORM/Tools/Pagination/WhereInWalkerTest.php b/tests/Doctrine/Tests/ORM/Tools/Pagination/WhereInWalkerTest.php
index 7291c2786..41152dc5d 100644
--- a/tests/Doctrine/Tests/ORM/Tools/Pagination/WhereInWalkerTest.php
+++ b/tests/Doctrine/Tests/ORM/Tools/Pagination/WhereInWalkerTest.php
@@ -121,5 +121,34 @@ class WhereInWalkerTest extends PaginationTestCase
             "SELECT u0_.id AS id_0, g1_.id AS id_1 FROM User u0_ INNER JOIN user_group u2_ ON u0_.id = u2_.user_id INNER JOIN groups g1_ ON g1_.id = u2_.group_id WHERE (NOT 1 = 2) AND u0_.id IN (?)", $whereInQuery->getSql()
         );
     }
+    
+    /**
+     * Arbitrary Join 
+     */
+    public function testWhereInQueryWithArbitraryJoin_NoWhere()
+    {
+        $whereInQuery  = $this->entityManager->createQuery(
+            'SELECT p FROM Doctrine\Tests\ORM\Tools\Pagination\BlogPost p JOIN Doctrine\Tests\ORM\Tools\Pagination\Category c WITH p.category = c'
+        );
+        $whereInQuery->setHint(Query::HINT_CUSTOM_TREE_WALKERS, array('Doctrine\ORM\Tools\Pagination\WhereInWalker'));
+        $whereInQuery->setHint(WhereInWalker::HINT_PAGINATOR_ID_COUNT, 10);
+
+        $this->assertEquals(
+            "SELECT b0_.id AS id_0, b0_.author_id AS author_id_1, b0_.category_id AS category_id_2 FROM BlogPost b0_ INNER JOIN Category c1_ ON (b0_.category_id = c1_.id) WHERE b0_.id IN (?)", $whereInQuery->getSql()
+        );
+    }
+    
+    public function testWhereInQueryWithArbitraryJoin_SingleWhere()
+    {
+        $whereInQuery = $this->entityManager->createQuery(
+            'SELECT p FROM Doctrine\Tests\ORM\Tools\Pagination\BlogPost p JOIN Doctrine\Tests\ORM\Tools\Pagination\Category c WITH p.category = c WHERE 1 = 1'
+        );
+        $whereInQuery->setHint(Query::HINT_CUSTOM_TREE_WALKERS, array('Doctrine\ORM\Tools\Pagination\WhereInWalker'));
+        $whereInQuery->setHint(WhereInWalker::HINT_PAGINATOR_ID_COUNT, 10);
+
+        $this->assertEquals(
+            "SELECT b0_.id AS id_0, b0_.author_id AS author_id_1, b0_.category_id AS category_id_2 FROM BlogPost b0_ INNER JOIN Category c1_ ON (b0_.category_id = c1_.id) WHERE 1 = 1 AND b0_.id IN (?)", $whereInQuery->getSql()
+        );
+    }
 }