diff --git a/dir.c b/dir.c
index 5415374105..2d0582e8a8 100644
--- a/dir.c
+++ b/dir.c
@@ -615,9 +615,12 @@ static void invalidate_gitignore(struct untracked_cache *uc,
 static void invalidate_directory(struct untracked_cache *uc,
 				 struct untracked_cache_dir *dir)
 {
+	int i;
 	uc->dir_invalidated++;
 	dir->valid = 0;
 	dir->untracked_nr = 0;
+	for (i = 0; i < dir->dirs_nr; i++)
+		dir->dirs[i]->recurse = 0;
 }
 
 /*
@@ -1578,6 +1581,10 @@ static int read_cached_dir(struct cached_dir *cdir)
 	}
 	while (cdir->nr_dirs < cdir->untracked->dirs_nr) {
 		struct untracked_cache_dir *d = cdir->untracked->dirs[cdir->nr_dirs];
+		if (!d->recurse) {
+			cdir->nr_dirs++;
+			continue;
+		}
 		cdir->ucd = d;
 		cdir->nr_dirs++;
 		return 0;
@@ -1599,8 +1606,10 @@ static void close_cached_dir(struct cached_dir *cdir)
 	 * We have gone through this directory and found no untracked
 	 * entries. Mark it valid.
 	 */
-	if (cdir->untracked)
+	if (cdir->untracked) {
 		cdir->untracked->valid = 1;
+		cdir->untracked->recurse = 1;
+	}
 }
 
 /*
@@ -1843,6 +1852,9 @@ static struct untracked_cache_dir *validate_untracked_cache(struct dir_struct *d
 		invalidate_gitignore(dir->untracked, root);
 		dir->untracked->ss_excludes_file = dir->ss_excludes_file;
 	}
+
+	/* Make sure this directory is not dropped out at saving phase */
+	root->recurse = 1;
 	return root;
 }
 
diff --git a/dir.h b/dir.h
index ff3d99bcb0..95baf014ca 100644
--- a/dir.h
+++ b/dir.h
@@ -115,8 +115,9 @@ struct untracked_cache_dir {
 	unsigned int untracked_alloc, dirs_nr, dirs_alloc;
 	unsigned int untracked_nr;
 	unsigned int check_only : 1;
-	/* all data in this struct are good */
+	/* all data except 'dirs' in this struct are good */
 	unsigned int valid : 1;
+	unsigned int recurse : 1;
 	/* null SHA-1 means this directory does not have .gitignore */
 	unsigned char exclude_sha1[20];
 	char name[FLEX_ARRAY];