diff --git a/fortitude_linter/fortitude_launcher.py b/fortitude_linter/fortitude_launcher.py
index f8a5f0d8..ecb9adef 100755
--- a/fortitude_linter/fortitude_launcher.py
+++ b/fortitude_linter/fortitude_launcher.py
@@ -52,7 +52,8 @@ def launch_fortitude(
 
     for top_dir_path in source_path.iterdir():
         # e.g. applications,science,interfaces
-        if not top_dir_path.is_dir():  # don't try to loop over files
+        # don't try to loop over files or hidden directories
+        if not top_dir_path.is_dir() or str(top_dir_path.name).startswith("."):
             continue
         for app_path in top_dir_path.iterdir():
             # e.g. adjoint_tests, adjoint, coupled_interface