diff --git a/builtin/clean.c b/builtin/clean.c
index 4ca12bc0c0..3ca940f83a 100644
--- a/builtin/clean.c
+++ b/builtin/clean.c
@@ -954,7 +954,7 @@ int cmd_clean(int argc, const char **argv, const char *prefix)
 		remove_directories = 1;
 	}
 
-	if (remove_directories)
+	if (remove_directories && !ignored_only)
 		dir.flags |= DIR_SHOW_IGNORED_TOO | DIR_KEEP_UNTRACKED_CONTENTS;
 
 	if (read_cache() < 0)
diff --git a/dir.c b/dir.c
index 6fb2f8ecdd..a3ad9702d6 100644
--- a/dir.c
+++ b/dir.c
@@ -193,6 +193,10 @@ int fill_directory(struct dir_struct *dir,
 	const char *prefix;
 	size_t prefix_len;
 
+	unsigned exclusive_flags = DIR_SHOW_IGNORED | DIR_SHOW_IGNORED_TOO;
+	if ((dir->flags & exclusive_flags) == exclusive_flags)
+		BUG("DIR_SHOW_IGNORED and DIR_SHOW_IGNORED_TOO are exclusive");
+
 	/*
 	 * Calculate common prefix for the pathspec, and
 	 * use that to optimize the directory walk