diff --git a/lib/jekyll/cleaner.rb b/lib/jekyll/cleaner.rb
index 70bd2f79..2a00a737 100644
--- a/lib/jekyll/cleaner.rb
+++ b/lib/jekyll/cleaner.rb
@@ -94,11 +94,12 @@ module Jekyll
     # Private: Creates a regular expression from the config's keep_files array
     #
     # Examples
-    #   ['.git','.svn'] creates the following regex: /\/(\.git|\/.svn)/
+    #   ['.git','.svn'] with site.dest "/myblog/_site" creates 
+    #   the following regex: /\/myblog\/_site\/(\.git|\/.svn)/
     #
     # Returns the regular expression
     def keep_file_regex
-      Regexp.union(site.keep_files)
+      /#{Regexp.quote(site.dest)}\/(#{Regexp.union(site.keep_files).source})/
     end
   end
 end