diff --git a/pisi/util.py b/pisi/util.py
index 59cdcbb7..676b99db 100644
--- a/pisi/util.py
+++ b/pisi/util.py
@@ -500,7 +500,7 @@ def do_patch(sourceDir, patchFile, level = 0):
         (ret, out, err) = run_batch('quilt push')
     else:
         # run GNU patch to apply original patch into tree
-        (ret, out, err) = run_batch("patch -p%d < \"%s\"" % (level, patchFile))
+        (ret, out, err) = run_batch("patch --remove-empty-files -p%d < \"%s\"" % (level, patchFile))
 
     if ret:
         if out is None and err is None: