diff --git a/app/helpers/gitlab_markdown_helper.rb b/app/helpers/gitlab_markdown_helper.rb
index db5b4eacd1f8b4be75c6891319c54778593f46cd..c7f769cee6459043f0e36a7a40aae2bf1e4a80b8 100644
--- a/app/helpers/gitlab_markdown_helper.rb
+++ b/app/helpers/gitlab_markdown_helper.rb
@@ -63,10 +63,14 @@ module GitlabMarkdownHelper
     paths = extract_paths(text)
 
     paths.uniq.each do |file_path|
-      new_path = rebuild_path(file_path)
-      # Finds quoted path so we don't replace other mentions of the string
-      # eg. "doc/api" will be replaced and "/home/doc/api/text" won't
-      text.gsub!("\"#{file_path}\"", "\"/#{new_path}\"")
+      # If project does not have repository
+      # its nothing to rebuild
+      if @repository.exists? && !@repository.empty?
+        new_path = rebuild_path(file_path)
+        # Finds quoted path so we don't replace other mentions of the string
+        # eg. "doc/api" will be replaced and "/home/doc/api/text" won't
+        text.gsub!("\"#{file_path}\"", "\"/#{new_path}\"")
+      end
     end
 
     text
@@ -91,7 +95,12 @@ module GitlabMarkdownHelper
   end
 
   def link_to_ignore?(link)
-    ignored_protocols.map{ |protocol| link.include?(protocol) }.any?
+    if link =~ /\#\w+/
+      # ignore anchors like <a href="#my-header">
+      true
+    else
+      ignored_protocols.map{ |protocol| link.include?(protocol) }.any?
+    end
   end
 
   def ignored_protocols
@@ -169,7 +178,7 @@ module GitlabMarkdownHelper
   def current_sha
     if @commit
       @commit.id
-    else
+    elsif @repository && !@repository.empty?
       @repository.head_commit.sha
     end
   end
diff --git a/spec/helpers/gitlab_markdown_helper_spec.rb b/spec/helpers/gitlab_markdown_helper_spec.rb
index fc9d1ac90c0bb1bbab94beb93aadc88e470a5dd6..f176a393415d05a638b2fe0922f10acdf403119a 100644
--- a/spec/helpers/gitlab_markdown_helper_spec.rb
+++ b/spec/helpers/gitlab_markdown_helper_spec.rb
@@ -5,6 +5,7 @@ describe GitlabMarkdownHelper do
   include IssuesHelper
 
   let!(:project) { create(:project) }
+  let(:empty_project) { create(:empty_project) }
 
   let(:user)          { create(:user, username: 'gfm') }
   let(:commit)        { project.repository.commit }
@@ -506,6 +507,19 @@ describe GitlabMarkdownHelper do
     end
   end
 
+  describe "markdwon for empty repository" do
+    before do
+      @project = empty_project
+      @repository = empty_project.repository
+    end
+
+    it "should not touch relative urls" do
+      actual = "[GitLab API doc][GitLab readme]\n [GitLab readme]: doc/api/README.md\n"
+      expected = "<p><a href=\"doc/api/README.md\">GitLab API doc</a></p>\n"
+      markdown(actual).should match(expected)
+    end
+  end
+
   describe "#render_wiki_content" do
     before do
       @wiki = double('WikiPage')