diff --git a/src/cocoindex_code/indexer.py b/src/cocoindex_code/indexer.py
index e028103..14169f3 100644
--- a/src/cocoindex_code/indexer.py
+++ b/src/cocoindex_code/indexer.py
@@ -48,11 +48,20 @@ def _normalize_gitignore_lines(lines: Iterable[str], directory: PurePath) -> lis
         stripped = line.lstrip()
         if not stripped or stripped.startswith("#"):
             continue
-        if line.startswith("\\#") or line.startswith("\\!"):
-            line = line[1:]
-        negated = line.startswith("!")
-        if negated:
-            line = line[1:]
+        # A leading "\#" or "\!" escapes a literal '#'/'!' — such a line is
+        # neither a comment nor a negation. Detect the escape *before* the
+        # negation check, and KEEP the backslash so the emitted pattern stays
+        # escaped for pathspec. Stripping it would leave a bare leading "!"/"#"
+        # — fine when a "**/" prefix is added ("\!foo" -> "**/!foo"), but for a
+        # path-bearing pattern there is no such prefix ("\!dir/f" -> "!dir/f"),
+        # and GitIgnoreSpec would then read it back as a negation/comment.
+        escaped = line.startswith("\\#") or line.startswith("\\!")
+        if escaped:
+            negated = False
+        else:
+            negated = line.startswith("!")
+            if negated:
+                line = line[1:]
         body = line.strip()
         if not body:
             continue
diff --git a/tests/test_indexer_gitignore.py b/tests/test_indexer_gitignore.py
new file mode 100644
index 0000000..c749e7f
--- /dev/null
+++ b/tests/test_indexer_gitignore.py
@@ -0,0 +1,64 @@
+"""Unit tests for .gitignore line normalization in the indexer."""
+
+from __future__ import annotations
+
+from pathlib import PurePath
+
+from pathspec import GitIgnoreSpec
+
+from cocoindex_code.indexer import _normalize_gitignore_lines
+
+ROOT = PurePath(".")
+
+
+def test_plain_pattern_is_globbed() -> None:
+    assert _normalize_gitignore_lines(["build"], ROOT) == ["**/build"]
+
+
+def test_negation_is_preserved() -> None:
+    assert _normalize_gitignore_lines(["build", "!build/keep.txt"], ROOT) == [
+        "**/build",
+        "!build/keep.txt",
+    ]
+
+
+def test_escaped_hash_is_literal_not_comment() -> None:
+    # "\#notacomment" -> a file literally named "#notacomment". The escape is
+    # kept so GitIgnoreSpec does not read the pattern back as a comment.
+    assert _normalize_gitignore_lines(["\\#notacomment"], ROOT) == ["**/\\#notacomment"]
+
+
+def test_escaped_bang_is_literal_not_negation() -> None:
+    # Regression: "\!important" means "ignore a file literally named '!important'",
+    # NOT a negation, so it must not become a "!"-prefixed (negation) pattern.
+    assert _normalize_gitignore_lines(["\\!important"], ROOT) == ["**/\\!important"]
+
+
+def test_escaped_bang_does_not_re_include_unrelated_matches() -> None:
+    # End-to-end: a "\!important" line must not cancel an unrelated "important"
+    # ignore rule. Before the fix it normalized to "!**/important", which
+    # re-included every "important" file the previous line had ignored.
+    spec = GitIgnoreSpec.from_lines(
+        _normalize_gitignore_lines(["important", "\\!important"], ROOT)
+    )
+    assert spec.match_file("important") is True  # still ignored
+    assert spec.match_file("!important") is True  # literal file ignored too
+
+
+def test_subdirectory_prefix_is_applied() -> None:
+    assert _normalize_gitignore_lines(["\\!keep"], PurePath("sub/dir")) == [
+        "sub/dir/**/\\!keep"
+    ]
+
+
+def test_escaped_path_bearing_pattern_is_literal() -> None:
+    # An escaped pattern that contains a "/" is anchored (no "**/" prefix is
+    # added), so the leading "!"/"#" would sit at the very start of the emitted
+    # pattern. Keeping the backslash is what stops GitIgnoreSpec from reading it
+    # back as a negation ("\!dir/file") or a comment ("\#dir/file").
+    spec = GitIgnoreSpec.from_lines(
+        _normalize_gitignore_lines(["\\!dir/file", "\\#dir/other"], ROOT)
+    )
+    assert spec.match_file("dir/file") is False  # unescaped sibling, untouched
+    assert spec.match_file("!dir/file") is True  # literal "!dir/file" ignored
+    assert spec.match_file("#dir/other") is True  # literal "#dir/other" ignored