diff --git a/polly/utils/checkout_cloog.sh b/polly/utils/checkout_cloog.sh
index 971c02782f04df441ff366364bc3beb73a6fe2b5..27c977ae3dbc350b3d86a21100ca304c321e416f 100755
--- a/polly/utils/checkout_cloog.sh
+++ b/polly/utils/checkout_cloog.sh
@@ -65,6 +65,8 @@ ISL_DIR=${CLOOG_DIR}/isl
 if [ ${IS_GIT} -eq 0 ]
 then
   echo :: Performing initial checkout
+  # Remove the existing CLooG and ISL dirs to avoid crashing older git versions.
+  run rm -rf ${CLOOG_DIR} ${ISL_DIR}
   run git clone http://repo.or.cz/r/cloog.git ${CLOOG_DIR}
   run git clone http://repo.or.cz/r/isl.git ${ISL_DIR}
 fi