diff --git a/lib/jekyll/cleaner.rb b/lib/jekyll/cleaner.rb
index 6c89e2bc..cab94d55 100644
--- a/lib/jekyll/cleaner.rb
+++ b/lib/jekyll/cleaner.rb
@@ -95,11 +95,12 @@ 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: /\A\/myblog\/_site\/(\.git|\/.svn)/
     #
     # Returns the regular expression
     def keep_file_regex
-      Regexp.union(site.keep_files)
+      /\A#{Regexp.quote(site.dest)}\/(#{Regexp.union(site.keep_files).source})/
     end
   end
 end
diff --git a/test/test_cleaner.rb b/test/test_cleaner.rb
index 43d99503..2118c4f4 100644
--- a/test/test_cleaner.rb
+++ b/test/test_cleaner.rb
@@ -37,6 +37,40 @@ class TestCleaner < JekyllUnitTest
     end
   end
 
+  context "not-nested directory in keep_files and similary named directory not in keep_files" do
+    setup do
+      clear_dest
+
+      FileUtils.mkdir_p(dest_dir('.git/child_dir'))
+      FileUtils.mkdir_p(dest_dir('username.github.io'))
+      FileUtils.touch(File.join(dest_dir('.git'), 'index.html'))
+      FileUtils.touch(File.join(dest_dir('username.github.io'), 'index.html'))
+
+      @site = fixture_site
+      @site.keep_files = ['.git']
+
+      @cleaner = Cleaner.new(@site)
+      @cleaner.cleanup!
+    end
+
+    teardown do
+      FileUtils.rm_rf(dest_dir('.git'))
+      FileUtils.rm_rf(dest_dir('username.github.io'))
+    end
+
+    should "keep the file in the directory in keep_files" do
+      assert File.exist?(File.join(dest_dir('.git'), 'index.html'))
+    end
+
+    should "delete the file in the directory not in keep_files" do
+      assert !File.exist?(File.join(dest_dir('username.github.io'), 'index.html'))
+    end
+
+    should "delete the directory not in keep_files" do
+      assert !File.exist?(dest_dir('username.github.io'))
+    end
+  end
+
   context "directory containing no files and non-empty directories" do
     setup do
       clear_dest