diff --git a/lib/jekyll/cleaner.rb b/lib/jekyll/cleaner.rb
index 583fc844..0aa3cdfd 100644
--- a/lib/jekyll/cleaner.rb
+++ b/lib/jekyll/cleaner.rb
@@ -30,7 +30,7 @@ module Jekyll
       def existing_files
         files = Set.new
         Dir.glob(File.join(site.dest, "**", "*"), File::FNM_DOTMATCH) do |file|
-          files << file unless file =~ /\/\.{1,2}$/ || file =~ keep_file_regex
+          files << file unless file =~ /\/\.{1,2}$/ || file =~ keep_file_regex || keep_dirs.include?(file)
         end
         files
       end
@@ -49,7 +49,19 @@ module Jekyll
       #
       # Returns a Set with the directory paths
       def new_dirs
-        new_files.map { |file| File.dirname(file) }.to_set
+        new_files.map { |file| parent_dirs(file) }.flatten.to_set
+      end
+
+      # Private: The list of parent directories of a given file
+      #
+      # Returns an Array with the directory paths
+      def parent_dirs(file)
+        parent_dir = File.dirname(file)
+        if parent_dir == site.dest
+          []
+        else
+          [parent_dir] + parent_dirs(parent_dir)
+        end
       end
 
       # Private: The list of existing files that will be replaced by a directory during build
@@ -59,6 +71,14 @@ module Jekyll
         new_dirs.select { |dir| File.file?(dir) }.to_set
       end
 
+      # Private: The list of directories that need to be kept because they are parent directories
+      # of files specified in keep_files
+      #
+      # Returns a Set with the directory paths
+      def keep_dirs
+        site.keep_files.map{|file| parent_dirs(File.join(site.dest, file))}.flatten.to_set
+      end
+
       # Private: Creates a regular expression from the config's keep_files array
       #
       # Examples
diff --git a/test/test_cleaner.rb b/test/test_cleaner.rb
new file mode 100644
index 00000000..e9bcc0f5
--- /dev/null
+++ b/test/test_cleaner.rb
@@ -0,0 +1,77 @@
+require 'helper'
+
+class TestCleaner < Test::Unit::TestCase
+  context "directory in keep_files" do
+    setup do
+      clear_dest
+      stub(Jekyll).configuration do
+        Jekyll::Configuration::DEFAULTS.merge({'source' => source_dir, 'destination' => dest_dir})
+      end
+
+      FileUtils.mkdir_p(dest_dir('to_keep/child_dir'))
+      FileUtils.touch(File.join(dest_dir('to_keep'), 'index.html'))
+      FileUtils.touch(File.join(dest_dir('to_keep/child_dir'), 'index.html'))
+
+      @site = Site.new(Jekyll.configuration)
+      @site.keep_files = ['to_keep/child_dir']
+
+      @cleaner = Site::Cleaner.new(@site)
+      @cleaner.cleanup!
+    end
+
+    teardown do
+      FileUtils.rm_rf(dest_dir('to_keep'))
+    end
+
+    should "keep the parent directory" do
+      assert File.exist?(dest_dir('to_keep'))
+    end
+
+    should "keep the child directory" do
+      assert File.exist?(dest_dir('to_keep/child_dir'))
+    end
+
+    should "keep the file in the directory in keep_files" do
+      assert File.exist?(File.join(dest_dir('to_keep/child_dir'), 'index.html'))
+    end
+
+    should "delete the file in the directory not in keep_files" do
+      assert !File.exist?(File.join(dest_dir('to_keep'), 'index.html'))
+    end
+  end
+
+  context "directory containing no files and non-empty directories" do
+    setup do
+      clear_dest
+      stub(Jekyll).configuration do
+        Jekyll::Configuration::DEFAULTS.merge({'source' => source_dir, 'destination' => dest_dir})
+      end
+
+      FileUtils.mkdir_p(source_dir('no_files_inside/child_dir'))
+      FileUtils.touch(File.join(source_dir('no_files_inside/child_dir'), 'index.html'))
+
+      @site = Site.new(Jekyll.configuration)
+      @site.process
+
+      @cleaner = Site::Cleaner.new(@site)
+      @cleaner.cleanup!
+    end
+
+    teardown do
+      FileUtils.rm_rf(source_dir('no_files_inside'))
+      FileUtils.rm_rf(dest_dir('no_files_inside'))
+    end
+
+    should "keep the parent directory" do
+      assert File.exist?(dest_dir('no_files_inside'))
+    end
+
+    should "keep the child directory" do
+      assert File.exist?(dest_dir('no_files_inside/child_dir'))
+    end
+
+    should "keep the file" do
+      assert File.exist?(File.join(dest_dir('no_files_inside/child_dir'), 'index.html'))
+    end
+  end
+end