diff --git a/lib/Doctrine/ORM/Tools/Pagination/WhereInWalker.php b/lib/Doctrine/ORM/Tools/Pagination/WhereInWalker.php
index 5400ef247..3bfb7b3fb 100644
--- a/lib/Doctrine/ORM/Tools/Pagination/WhereInWalker.php
+++ b/lib/Doctrine/ORM/Tools/Pagination/WhereInWalker.php
@@ -120,7 +120,9 @@ class WhereInWalker extends TreeWalkerAdapter
                         $conditionalPrimary
                     ))
                 ));
-            } elseif ($AST->whereClause->conditionalExpression instanceof ConditionalExpression) {
+            } elseif ($AST->whereClause->conditionalExpression instanceof ConditionalExpression
+                || $AST->whereClause->conditionalExpression instanceof ConditionalFactor
+            ) {
                 $tmpPrimary = new ConditionalPrimary;
                 $tmpPrimary->conditionalExpression = $AST->whereClause->conditionalExpression;
                 $AST->whereClause->conditionalExpression = new ConditionalTerm(array(
diff --git a/tests/Doctrine/Tests/ORM/Tools/Pagination/WhereInWalkerTest.php b/tests/Doctrine/Tests/ORM/Tools/Pagination/WhereInWalkerTest.php
index d7bcd0e12..0db5d2587 100644
--- a/tests/Doctrine/Tests/ORM/Tools/Pagination/WhereInWalkerTest.php
+++ b/tests/Doctrine/Tests/ORM/Tools/Pagination/WhereInWalkerTest.php
@@ -107,5 +107,19 @@ class WhereInWalkerTest extends PaginationTestCase
                 "SELECT u0_.id AS id0, g1_.id AS id1 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 (1 = 1 AND 2 = 2 OR 3 = 3) AND u0_.id IN (?, ?, ?, ?, ?, ?, ?, ?, ?, ?)", $whereInQuery->getSql()
         );
     }
+
+    public function testWhereInQuery_WhereNot()
+    {
+        $query = $this->entityManager->createQuery(
+                        'SELECT u, g FROM Doctrine\Tests\ORM\Tools\Pagination\User u JOIN u.groups g WHERE NOT 1 = 2'
+        );
+        $whereInQuery = clone $query;
+        $whereInQuery->setHint(Query::HINT_CUSTOM_TREE_WALKERS, array('Doctrine\ORM\Tools\Pagination\WhereInWalker'));
+        $whereInQuery->setHint(WhereInWalker::HINT_PAGINATOR_ID_COUNT, 10);
+
+        $this->assertEquals(
+                "SELECT u0_.id AS id0, g1_.id AS id1 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()
+        );
+    }
 }