diff --git a/bin/jekyll b/bin/jekyll
index e712616b35d..b8467fb112d 100755
--- a/bin/jekyll
+++ b/bin/jekyll
@@ -145,6 +145,10 @@ opts = OptionParser.new do |opts|
     puts "Jekyll " + Jekyll::VERSION
     exit 0
   end
+
+  opts.on( "--keep-files filename1,filename2", Array, "Whether to keep files that match the filename (default: .git)") do |names|
+    options['keep_files'] = names
+  end
 end
 
 # Read command line options into `options` hash
diff --git a/lib/jekyll.rb b/lib/jekyll.rb
index eef5ab1cbed..2e5a681e733 100644
--- a/lib/jekyll.rb
+++ b/lib/jekyll.rb
@@ -60,6 +60,7 @@ module Jekyll
     'destination'   => File.join(Dir.pwd, '_site'),
     'plugins'       => File.join(Dir.pwd, '_plugins'),
     'layouts'       => '_layouts',
+    'keep_files'   => ['.git','.svn'],
 
     'future'        => true,
     'lsi'           => false,
diff --git a/lib/jekyll/site.rb b/lib/jekyll/site.rb
index 7dbf1336aac..6afa3c9e57b 100644
--- a/lib/jekyll/site.rb
+++ b/lib/jekyll/site.rb
@@ -5,7 +5,8 @@ module Jekyll
   class Site
     attr_accessor :config, :layouts, :posts, :pages, :static_files,
                   :categories, :exclude, :include, :source, :dest, :lsi, :pygments,
-                  :permalink_style, :tags, :time, :future, :safe, :plugins, :limit_posts
+                  :permalink_style, :tags, :time, :future, :safe, :plugins, :limit_posts,
+                  :keep_files
 
     attr_accessor :converters, :generators
 
@@ -26,6 +27,7 @@ def initialize(config)
       self.include         = config['include'] || []
       self.future          = config['future']
       self.limit_posts     = config['limit_posts'] || nil
+      self.keep_files      = config['keep_files'] || []
 
       self.reset
       self.setup
@@ -222,8 +224,12 @@ def render
     def cleanup
       # all files and directories in destination, including hidden ones
       dest_files = Set.new
-      Dir.glob(File.join(self.dest, "**", "*")) do |file|
-        dest_files << file
+      Dir.glob(File.join(self.dest, "**", "*"), File::FNM_DOTMATCH) do |file|
+        if self.keep_files.length > 0
+          dest_files << file unless file =~ /\/\.{1,2}$/ || file =~ keep_file_regex
+        else
+          dest_files << file unless file =~ /\/\.{1,2}$/
+        end
       end
 
       # files to be written
@@ -244,10 +250,21 @@ def cleanup
       files.merge(dirs)
 
       obsolete_files = dest_files - files
-
       FileUtils.rm_rf(obsolete_files.to_a)
     end
 
+    # Private: creates a regular expression from the keep_files array
+    # 
+    # Examples
+    #   ['.git','.svn'] creates the following regex: /\/(\.git|\/.svn)/
+    #
+    # Returns the regular expression
+    def keep_file_regex
+      or_list = self.keep_files.join("|")
+      pattern = "\/(#{or_list.gsub(".", "\.")})"
+      Regexp.new pattern
+    end
+
     # Write static files, pages, and posts.
     #
     # Returns nothing.
diff --git a/test/test_site.rb b/test/test_site.rb
index 03f1886e3d1..f71a95996f5 100644
--- a/test/test_site.rb
+++ b/test/test_site.rb
@@ -200,12 +200,22 @@ class TestSite < Test::Unit::TestCase
         File.open(dest_dir('qux/obsolete.html'), 'w')
         # empty directory
         FileUtils.mkdir(dest_dir('quux'))
+        FileUtils.mkdir(dest_dir('.git'))
+        FileUtils.mkdir(dest_dir('.svn'))
+        FileUtils.mkdir(dest_dir('.hg'))
+        # single file in repository
+        File.open(dest_dir('.git/HEAD'), 'w')
+        File.open(dest_dir('.svn/HEAD'), 'w')
+        File.open(dest_dir('.hg/HEAD'), 'w')
       end
       
       teardown do
         FileUtils.rm_f(dest_dir('obsolete.html'))
         FileUtils.rm_rf(dest_dir('qux'))
         FileUtils.rm_f(dest_dir('quux'))
+        FileUtils.rm_rf(dest_dir('.git'))
+        FileUtils.rm_rf(dest_dir('.svn'))
+        FileUtils.rm_rf(dest_dir('.hg'))
       end
       
       should 'remove orphaned files in destination' do
@@ -213,6 +223,22 @@ class TestSite < Test::Unit::TestCase
         assert !File.exist?(dest_dir('obsolete.html'))
         assert !File.exist?(dest_dir('qux'))
         assert !File.exist?(dest_dir('quux'))
+        assert File.exist?(dest_dir('.git'))
+        assert File.exist?(dest_dir('.git/HEAD'))
+      end
+
+      should 'remove orphaned files in destination - keep_files .svn' do
+        config = Jekyll::DEFAULTS.merge({'source' => source_dir, 'destination' => dest_dir, 'keep_files' => ['.svn']})
+        @site = Site.new(config)
+        @site.process
+        assert !File.exist?(dest_dir('.htpasswd'))
+        assert !File.exist?(dest_dir('obsolete.html'))
+        assert !File.exist?(dest_dir('qux'))
+        assert !File.exist?(dest_dir('quux'))
+        assert !File.exist?(dest_dir('.git'))
+        assert !File.exist?(dest_dir('.git/HEAD'))
+        assert File.exist?(dest_dir('.svn'))
+        assert File.exist?(dest_dir('.svn/HEAD'))
       end
 
     end