diff --git a/rhodecode/lib/helpers.py b/rhodecode/lib/helpers.py
--- a/rhodecode/lib/helpers.py
+++ b/rhodecode/lib/helpers.py
@@ -1602,16 +1602,24 @@ def urlify_commits(text_, repository):
 
 
 def _process_url_func(match_obj, repo_name, uid, entry,
-                      return_raw_data=False):
+                      return_raw_data=False, link_format='html'):
     pref = ''
     if match_obj.group().startswith(' '):
         pref = ' '
 
     issue_id = ''.join(match_obj.groups())
-    tmpl = (
-        '%(pref)s<a class="%(cls)s" href="%(url)s">'
-        '%(issue-prefix)s%(id-repr)s'
-        '</a>')
+
+    if link_format == 'html':
+        tmpl = (
+            '%(pref)s<a class="%(cls)s" href="%(url)s">'
+            '%(issue-prefix)s%(id-repr)s'
+            '</a>')
+    elif link_format == 'rst':
+        tmpl = '`%(issue-prefix)s%(id-repr)s <%(url)s>`_'
+    elif link_format == 'markdown':
+        tmpl = '[%(issue-prefix)s%(id-repr)s](%(url)s)'
+    else:
+        raise ValueError('Bad link_format:{}'.format(link_format))
 
     (repo_name_cleaned,
      parent_group_name) = RepoGroupModel().\
@@ -1644,7 +1652,12 @@ def _process_url_func(match_obj, repo_na
     return tmpl % data
 
 
-def process_patterns(text_string, repo_name, config=None):
+def process_patterns(text_string, repo_name, link_format='html'):
+    allowed_formats = ['html', 'rst', 'markdown']
+    if link_format not in allowed_formats:
+        raise ValueError('Link format can be only one of:{} got {}'.format(
+                         allowed_formats, link_format))
+
     repo = None
     if repo_name:
         # Retrieving repo_name to avoid invalid repo_name to explode on
@@ -1656,6 +1669,7 @@ def process_patterns(text_string, repo_n
 
     issues_data = []
     newtext = text_string
+
     for uid, entry in active_entries.items():
         log.debug('found issue tracker entry with uid %s' % (uid,))
 
@@ -1682,7 +1696,8 @@ def process_patterns(text_string, repo_n
             issues_data.append(data_func(match_obj))
 
         url_func = partial(
-            _process_url_func, repo_name=repo_name, entry=entry, uid=uid)
+            _process_url_func, repo_name=repo_name, entry=entry, uid=uid,
+            link_format=link_format)
 
         newtext = pattern.sub(url_func, newtext)
         log.debug('processed prefix:uid `%s`' % (uid,))
@@ -1750,7 +1765,8 @@ def renderer_from_filename(filename, exc
     return None
 
 
-def render(source, renderer='rst', mentions=False, relative_url=None):
+def render(source, renderer='rst', mentions=False, relative_url=None,
+           repo_name=None):
 
     def maybe_convert_relative_links(html_source):
         if relative_url:
@@ -1758,11 +1774,21 @@ def render(source, renderer='rst', menti
         return html_source
 
     if renderer == 'rst':
+        if repo_name:
+            # process patterns on comments if we pass in repo name
+            source, issues = process_patterns(
+                source, repo_name, link_format='rst')
+
         return literal(
             '<div class="rst-block">%s</div>' %
             maybe_convert_relative_links(
                 MarkupRenderer.rst(source, mentions=mentions)))
     elif renderer == 'markdown':
+        if repo_name:
+            # process patterns on comments if we pass in repo name
+            source, issues = process_patterns(
+                source, repo_name, link_format='markdown')
+
         return literal(
             '<div class="markdown-block">%s</div>' %
             maybe_convert_relative_links(
diff --git a/rhodecode/tests/lib/test_helpers.py b/rhodecode/tests/lib/test_helpers.py
--- a/rhodecode/tests/lib/test_helpers.py
+++ b/rhodecode/tests/lib/test_helpers.py
@@ -103,55 +103,62 @@ def test_extract_issues(backend, text_st
     assert issues == expected
 
 
-@pytest.mark.parametrize('text_string, pattern, expected_text', [
-    ('Fix #42', '(?:#)(?P<issue_id>\d+)',
-     'Fix <a class="issue-tracker-link" href="http://r.io/{repo}/i/42">#42</a>'
-     ),
-    ('Fix #42', '(?:#)?<issue_id>\d+)', 'Fix #42'),  # Broken regex
+@pytest.mark.parametrize('text_string, pattern, link_format, expected_text', [
+    ('Fix #42', '(?:#)(?P<issue_id>\d+)', 'html',
+     'Fix <a class="issue-tracker-link" href="http://r.io/{repo}/i/42">#42</a>'),
+
+    ('Fix #42', '(?:#)(?P<issue_id>\d+)', 'markdown',
+     'Fix [#42](http://r.io/{repo}/i/42)'),
+
+    ('Fix #42', '(?:#)(?P<issue_id>\d+)', 'rst',
+     'Fix `#42 <http://r.io/{repo}/i/42>`_'),
+
+    ('Fix #42', '(?:#)?<issue_id>\d+)', 'html',
+     'Fix #42'),  # Broken regex
 ])
-def test_process_patterns_repo(backend, text_string, pattern, expected_text):
+def test_process_patterns_repo(backend, text_string, pattern, expected_text, link_format):
     repo = backend.create_repo()
-    config = {'123': {
-        'uid': '123',
-        'pat': pattern,
-        'url': 'http://r.io/${repo}/i/${issue_id}',
-        'pref': '#',
-        }
-    }
 
     def get_settings_mock(self, cache=True):
-        return config
+        return {
+            '123': {
+                'uid': '123',
+                'pat': pattern,
+                'url': 'http://r.io/${repo}/i/${issue_id}',
+                'pref': '#',
+            }
+        }
 
     with mock.patch.object(IssueTrackerSettingsModel,
                            'get_settings', get_settings_mock):
         processed_text, issues = helpers.process_patterns(
-            text_string, repo.repo_name, config)
+            text_string, repo.repo_name, link_format)
 
     assert processed_text == expected_text.format(repo=repo.repo_name)
 
 
 @pytest.mark.parametrize('text_string, pattern, expected_text', [
     ('Fix #42', '(?:#)(?P<issue_id>\d+)',
-     'Fix <a class="issue-tracker-link" href="http://r.io/i/42">#42</a>'
-     ),
-    ('Fix #42', '(?:#)?<issue_id>\d+)', 'Fix #42'),  # Broken regex
+     'Fix <a class="issue-tracker-link" href="http://r.io/i/42">#42</a>'),
+    ('Fix #42', '(?:#)?<issue_id>\d+)',
+     'Fix #42'),  # Broken regex
 ])
 def test_process_patterns_no_repo(text_string, pattern, expected_text):
-    config = {'123': {
-        'uid': '123',
-        'pat': pattern,
-        'url': 'http://r.io/i/${issue_id}',
-        'pref': '#',
-        }
-    }
 
     def get_settings_mock(self, cache=True):
-        return config
+        return {
+            '123': {
+                'uid': '123',
+                'pat': pattern,
+                'url': 'http://r.io/i/${issue_id}',
+                'pref': '#',
+            }
+        }
 
     with mock.patch.object(IssueTrackerSettingsModel,
                            'get_global_settings', get_settings_mock):
         processed_text, issues = helpers.process_patterns(
-            text_string, '', config)
+            text_string, '')
 
     assert processed_text == expected_text
 
@@ -161,21 +168,21 @@ def test_process_patterns_non_existent_r
     pattern = '(?:#)(?P<issue_id>\d+)'
     expected_text = ('Fix <a class="issue-tracker-link" '
                      'href="http://r.io/do-not-exist/i/42">#42</a>')
-    config = {'123': {
-        'uid': '123',
-        'pat': pattern,
-        'url': 'http://r.io/${repo}/i/${issue_id}',
-        'pref': '#',
-        }
-    }
 
     def get_settings_mock(self, cache=True):
-        return config
+        return {
+            '123': {
+                'uid': '123',
+                'pat': pattern,
+                'url': 'http://r.io/${repo}/i/${issue_id}',
+                'pref': '#',
+            }
+        }
 
     with mock.patch.object(IssueTrackerSettingsModel,
                            'get_global_settings', get_settings_mock):
         processed_text, issues = helpers.process_patterns(
-            text_string, 'do-not-exist', config)
+            text_string, 'do-not-exist')
 
     assert processed_text == expected_text