diff --git a/Library/Homebrew/keg.rb b/Library/Homebrew/keg.rb
index f6a051a954..3d8b08d203 100644
--- a/Library/Homebrew/keg.rb
+++ b/Library/Homebrew/keg.rb
@@ -316,7 +316,7 @@ class Keg
     unless dry_run
       remove_old_aliases
       remove_linked_keg_record if linked?
-      dirs.reverse_each(&:rmdir_if_possible)
+      (dirs - MUST_EXIST_SUBDIRECTORIES).reverse_each(&:rmdir_if_possible)
     end
 
     ObserverPathnameExtension.n