diff --git a/codex-rs/core-skills/src/loader/environment.rs b/codex-rs/core-skills/src/loader/environment.rs
index da525d3362..8d400d7cdc 100644
--- a/codex-rs/core-skills/src/loader/environment.rs
+++ b/codex-rs/core-skills/src/loader/environment.rs
@@ -160,6 +160,7 @@ pub async fn load_environment_skills_from_root(
                 max_directories: MAX_SKILLS_DIRS_PER_ROOT,
                 max_entries: MAX_SKILLS_ENTRIES_PER_ROOT,
                 follow_directory_symlinks: true,
+                prune_hidden_directories: false,
             },
             /*sandbox*/ None,
         )
diff --git a/codex-rs/exec-server/tests/file_system/shared.rs b/codex-rs/exec-server/tests/file_system/shared.rs
index 261c6b07d0..236a9623ee 100644
--- a/codex-rs/exec-server/tests/file_system/shared.rs
+++ b/codex-rs/exec-server/tests/file_system/shared.rs
@@ -402,6 +402,7 @@ async fn file_system_walk_returns_a_bounded_tree(
                 max_directories: 10,
                 max_entries: 10,
                 follow_directory_symlinks: false,
+                prune_hidden_directories: false,
             },
             /*sandbox*/ None,
         )
@@ -447,6 +448,7 @@ async fn file_system_walk_returns_a_bounded_tree(
                 max_directories: 10,
                 max_entries: 10,
                 follow_directory_symlinks: false,
+                prune_hidden_directories: false,
             },
             /*sandbox*/ None,
         )
@@ -469,6 +471,7 @@ async fn file_system_walk_returns_a_bounded_tree(
                 max_directories: 1,
                 max_entries: 10,
                 follow_directory_symlinks: false,
+                prune_hidden_directories: false,
             },
             /*sandbox*/ None,
         )
@@ -491,6 +494,7 @@ async fn file_system_walk_returns_a_bounded_tree(
                 max_directories: 10,
                 max_entries: 1,
                 follow_directory_symlinks: false,
+                prune_hidden_directories: false,
             },
             /*sandbox*/ None,
         )
@@ -535,6 +539,7 @@ async fn file_system_walk_honors_read_sandbox(
                 max_directories: 2,
                 max_entries: 2,
                 follow_directory_symlinks: false,
+                prune_hidden_directories: false,
             },
             Some(&sandbox),
         )
diff --git a/codex-rs/exec-server/tests/file_system_unix.rs b/codex-rs/exec-server/tests/file_system_unix.rs
index f658045441..c3fc680787 100644
--- a/codex-rs/exec-server/tests/file_system_unix.rs
+++ b/codex-rs/exec-server/tests/file_system_unix.rs
@@ -299,6 +299,7 @@ async fn file_system_walk_handles_directory_symlinks(
                 max_directories: 4,
                 max_entries: 8,
                 follow_directory_symlinks: false,
+                prune_hidden_directories: false,
             },
             /*sandbox*/ None,
         )
@@ -321,6 +322,7 @@ async fn file_system_walk_handles_directory_symlinks(
                 max_directories: 4,
                 max_entries: 8,
                 follow_directory_symlinks: true,
+                prune_hidden_directories: false,
             },
             /*sandbox*/ None,
         )
@@ -351,6 +353,68 @@ async fn file_system_walk_handles_directory_symlinks(
     Ok(())
 }
 
+#[test_case(FileSystemImplementation::Local ; "local")]
+#[test_case(FileSystemImplementation::Remote ; "remote")]
+#[tokio::test(flavor = "multi_thread", worker_threads = 2)]
+async fn file_system_walk_prunes_hidden_directories_without_claiming_visible_aliases(
+    implementation: FileSystemImplementation,
+) -> Result<()> {
+    let context = create_file_system_context(implementation).await?;
+    let file_system = context.file_system;
+
+    let tmp = TempDir::new()?;
+    let root = tmp.path().join("root");
+    let hidden = root.join(".hidden");
+    let hidden_nested = hidden.join("nested");
+    let visible = root.join("visible");
+    std::fs::create_dir_all(&hidden_nested)?;
+    std::fs::write(hidden_nested.join("note.txt"), "visible through alias")?;
+    symlink(&hidden, &visible)?;
+
+    let outcome = file_system
+        .walk(
+            &PathUri::from_host_native_path(&root)?,
+            WalkOptions {
+                max_depth: 3,
+                max_directories: 3,
+                max_entries: 6,
+                follow_directory_symlinks: true,
+                prune_hidden_directories: true,
+            },
+            /*sandbox*/ None,
+        )
+        .await
+        .with_context(|| format!("mode={implementation}"))?;
+
+    assert_eq!(
+        outcome,
+        WalkOutcome {
+            entries: vec![
+                WalkEntry {
+                    path: PathUri::from_host_native_path(hidden)?,
+                    kind: WalkEntryKind::Directory,
+                },
+                WalkEntry {
+                    path: PathUri::from_host_native_path(&visible)?,
+                    kind: WalkEntryKind::Directory,
+                },
+                WalkEntry {
+                    path: PathUri::from_host_native_path(visible.join("nested"))?,
+                    kind: WalkEntryKind::Directory,
+                },
+                WalkEntry {
+                    path: PathUri::from_host_native_path(visible.join("nested/note.txt"))?,
+                    kind: WalkEntryKind::File,
+                },
+            ],
+            errors: Vec::new(),
+            truncated: false,
+        }
+    );
+
+    Ok(())
+}
+
 #[test_case(FileSystemImplementation::Local ; "local")]
 #[test_case(FileSystemImplementation::Remote ; "remote")]
 #[tokio::test(flavor = "multi_thread", worker_threads = 2)]
diff --git a/codex-rs/file-system/src/lib.rs b/codex-rs/file-system/src/lib.rs
index 737412f463..2ef3bcf710 100644
--- a/codex-rs/file-system/src/lib.rs
+++ b/codex-rs/file-system/src/lib.rs
@@ -81,6 +81,9 @@ pub struct WalkOptions {
     pub max_entries: usize,
     /// Whether directory symlinks should be followed.
     pub follow_directory_symlinks: bool,
+    /// Whether directories whose names start with `.` should be returned but not traversed.
+    #[serde(default, skip_serializing_if = "std::ops::Not::not")]
+    pub prune_hidden_directories: bool,
 }
 
 /// Type of a filesystem entry returned by a walk.
@@ -463,6 +466,9 @@ async fn walk_via_directory_reads<F: ExecutorFileSystem + ?Sized>(
             });
 
             if kind == WalkEntryKind::Directory && depth < options.max_depth {
+                if options.prune_hidden_directories && entry.file_name.starts_with('.') {
+                    continue;
+                }
                 let directory_identity = if options.follow_directory_symlinks {
                     match file_system.canonicalize(&path, sandbox).await {
                         Ok(path) => path,