diff --git a/app/helpers/gitlab_markdown_helper.rb b/app/helpers/gitlab_markdown_helper.rb
index d89f7b4a28d..3c207619adf 100644
--- a/app/helpers/gitlab_markdown_helper.rb
+++ b/app/helpers/gitlab_markdown_helper.rb
@@ -1,3 +1,5 @@
+require 'nokogiri'
+
 module GitlabMarkdownHelper
   include Gitlab::Markdown
 
@@ -21,11 +23,22 @@ module GitlabMarkdownHelper
 
     gfm_body = gfm(escaped_body, {}, html_options)
 
-    gfm_body.gsub!(%r{<a.*?>.*?</a>}m) do |match|
-      "</a>#{match}#{link_to("", url, html_options)[0..-5]}" # "</a>".length +1
+    fragment = Nokogiri::XML::DocumentFragment.parse(gfm_body)
+    if fragment.children.size == 1 && fragment.children[0].name == 'a'
+      # Fragment has only one node, and it's a link generated by `gfm`.
+      # Replace it with our requested link.
+      text = fragment.children[0].text
+      fragment.children[0].replace(link_to(text, url, html_options))
+    else
+      # Traverse the fragment's first generation of children looking for pure
+      # text, wrapping anything found in the requested link
+      fragment.children.each do |node|
+        next unless node.text?
+        node.replace(link_to(node.text, url, html_options))
+      end
     end
 
-    link_to(gfm_body.html_safe, url, html_options)
+    fragment.to_html.html_safe
   end
 
   def markdown(text, options={})
diff --git a/spec/helpers/gitlab_markdown_helper_spec.rb b/spec/helpers/gitlab_markdown_helper_spec.rb
index d0b200a9ff8..bbb434638ce 100644
--- a/spec/helpers/gitlab_markdown_helper_spec.rb
+++ b/spec/helpers/gitlab_markdown_helper_spec.rb
@@ -94,6 +94,12 @@ describe GitlabMarkdownHelper do
       expect(link_to_gfm(actual, commit_path)).
         to match('&lt;h1&gt;test&lt;/h1&gt;')
     end
+
+    it 'ignores reference links when they are the entire body' do
+      text = issues[0].to_reference
+      act = link_to_gfm(text, '/foo')
+      expect(act).to eq %Q(<a href="/foo">#{issues[0].to_reference}</a>)
+    end
   end
 
   describe '#render_wiki_content' do