diff --git a/llama-index-core/llama_index/core/readers/file/base.py b/llama-index-core/llama_index/core/readers/file/base.py
index efd9ff34b49b8..a20e7d2b7e5db 100644
--- a/llama-index-core/llama_index/core/readers/file/base.py
+++ b/llama-index-core/llama_index/core/readers/file/base.py
@@ -249,7 +249,9 @@ def _add_files(self, input_dir: Path) -> List[Path]:
             # in glob for backwards compatibility.
             ref = Path(ref)
             is_dir = self.fs.isdir(ref)
-            skip_because_hidden = self.exclude_hidden and self.is_hidden(ref)
+            skip_because_hidden = self.exclude_hidden and self.is_hidden(
+                ref.relative_to(input_dir.absolute())
+            )
             skip_because_bad_ext = (
                 self.required_exts is not None and ref.suffix not in self.required_exts
             )