diff --git a/src/yatl/utils/file_utils.py b/src/yatl/utils/file_utils.py
index b385b07..30ebc00 100644
--- a/src/yatl/utils/file_utils.py
+++ b/src/yatl/utils/file_utils.py
@@ -51,6 +51,15 @@ def load_test_yaml(file_path: str) -> dict[str, str | int | list[Any]] | bool:
         raise InvalidYamlError(f"Encoding error in {file_path}: {e}")
 
 
+def _is_effectively_empty(file_path: str) -> bool:
+    """Return whether a YAML file contains only whitespace or comments."""
+    try:
+        with open(file_path, encoding="utf-8") as f:
+            return all(not line.strip() or line.lstrip().startswith("#") for line in f)
+    except UnicodeDecodeError:
+        return False
+
+
 def search_files(base_path: str) -> list[str]:
     """Searches for test files with a .yatl.yaml/.yatl.yml suffix.
 
@@ -67,7 +76,9 @@ def search_files(base_path: str) -> list[str]:
         DirectoryNotFoundError: If base_path is neither a file nor a directory.
     """
     if os.path.isfile(base_path):
-        if base_path.endswith(".yatl.yaml") or base_path.endswith(".yatl.yml"):
+        if (
+            base_path.endswith(".yatl.yaml") or base_path.endswith(".yatl.yml")
+        ) and not _is_effectively_empty(base_path):
             return [base_path]
         return []
 
@@ -79,8 +90,10 @@ def search_files(base_path: str) -> list[str]:
     def _search(current_path: str):
         for item in os.listdir(current_path):
             full_path = os.path.join(current_path, item)
-            if os.path.isfile(full_path) and (
-                item.endswith(".yatl.yaml") or item.endswith(".yatl.yml")
+            if (
+                os.path.isfile(full_path)
+                and (item.endswith(".yatl.yaml") or item.endswith(".yatl.yml"))
+                and not _is_effectively_empty(full_path)
             ):
                 files.append(full_path)
             elif os.path.isdir(full_path):
diff --git a/tests/test_cli/test_command.py b/tests/test_cli/test_command.py
index 8e7dbcc..e48f78f 100644
--- a/tests/test_cli/test_command.py
+++ b/tests/test_cli/test_command.py
@@ -83,3 +83,19 @@ def test_skip(fixture_path):
     assert result.returncode == 0, (
         f"yatl exited with code {result.returncode}\nstdout: {result.stdout}\n"
     )
+
+
+def test_empty_test_files_are_ignored(tmp_path):
+    empty_test = tmp_path / "empty.yatl.yaml"
+    empty_test.write_text("", encoding="utf-8")
+
+    result = subprocess.run(
+        [sys.executable, "-m", "yatl", str(tmp_path)],
+        capture_output=True,
+        text=True,
+    )
+
+    assert result.returncode == 0
+    assert "No .yatl.yaml files found" in result.stdout
+    assert "Run test:" not in result.stdout
+    assert "Test passed" not in result.stdout
diff --git a/tests/test_run.py b/tests/test_run.py
index ac13f8e..9b86247 100644
--- a/tests/test_run.py
+++ b/tests/test_run.py
@@ -49,6 +49,16 @@ def test_search_files():
     assert len(files) == 2
 
 
+@pytest.mark.parametrize("content", ["", "  \n\t", "# comment\n  # another comment\n"])
+def test_search_files_ignores_empty_yaml_files(tmp_path, content):
+    "Test that empty YAML files are excluded from test discovery."
+    empty_test = tmp_path / "empty.yatl.yaml"
+    empty_test.write_text(content, encoding="utf-8")
+
+    assert search_files(str(tmp_path)) == []
+    assert search_files(str(empty_test)) == []
+
+
 def test_search_files_with_invalid_path():
     "Test that search_files raises a clear error with invalid path."
     with pytest.raises(