diff --git a/pelican/generators.py b/pelican/generators.py
index 8d6de666..f6ac35a0 100755
--- a/pelican/generators.py
+++ b/pelican/generators.py
@@ -161,20 +161,6 @@ class ArticlesGenerator(Generator):
         # in writer, articles pass first
         article_template = self.get_template('article')
         for article in chain(self.translations, self.articles):
-            add_to_url = u''
-            if 'ARTICLE_PERMALINK_STRUCTURE' in self.settings:
-                article_permalink_structure = self.settings['ARTICLE_PERMALINK_STRUCTURE']
-                article_permalink_structure = article_permalink_structure.lstrip('/')
-
-                # try to substitute any python datetime directive
-                add_to_url = article.date.strftime(article_permalink_structure)
-                # try to substitute any article metadata in rest file
-                add_to_url = add_to_url % article.__dict__
-                add_to_url = [slugify(i) for i in add_to_url.split('/')]
-                add_to_url = os.path.join(*add_to_url)
-
-            article.url = urlparse.urljoin(add_to_url, article.url)
-            article.save_as = urlparse.urljoin(add_to_url, article.save_as)
             write(article.save_as,
                           article_template, self.context, article=article,
                           category=article.category)
@@ -247,6 +233,21 @@ class ArticlesGenerator(Generator):
             if not is_valid_content(article, f):
                 continue
 
+            add_to_url = u''
+            if 'ARTICLE_PERMALINK_STRUCTURE' in self.settings:
+                article_permalink_structure = self.settings['ARTICLE_PERMALINK_STRUCTURE']
+                article_permalink_structure = article_permalink_structure.lstrip('/')
+
+                # try to substitute any python datetime directive
+                add_to_url = article.date.strftime(article_permalink_structure)
+                # try to substitute any article metadata in rest file
+                add_to_url = add_to_url % article.__dict__
+                add_to_url = [slugify(i) for i in add_to_url.split('/')]
+                add_to_url = os.path.join(*add_to_url)
+
+            article.url = urlparse.urljoin(add_to_url, article.url)
+            article.save_as = urlparse.urljoin(add_to_url, article.save_as)
+
             if article.status == "published":
                 if hasattr(article, 'tags'):
                     for tag in article.tags:
diff --git a/pelican/themes/notmyidea/templates/comments.html b/pelican/themes/notmyidea/templates/comments.html
index ea693afb..bb033c0f 100644
--- a/pelican/themes/notmyidea/templates/comments.html
+++ b/pelican/themes/notmyidea/templates/comments.html
@@ -1 +1 @@
-{% if DISQUS_SITENAME %}<p>There are <a href="{{ SITEURL }}/{{ article.slug }}.html#disqus_thread">comments</a>.</p>{% endif %}
+{% if DISQUS_SITENAME %}<p>There are <a href="{{ SITEURL }}/{{ article.url }}#disqus_thread">comments</a>.</p>{% endif %}
diff --git a/pelican/themes/simple/templates/article.html b/pelican/themes/simple/templates/article.html
index 0bfed07a..30d31fb6 100644
--- a/pelican/themes/simple/templates/article.html
+++ b/pelican/themes/simple/templates/article.html
@@ -1,7 +1,7 @@
 {% extends "base.html" %}
 {% block content %}        
 <section id="content" class="body">    
-        <header> <h2 class="entry-title"><a href="{{ article.url }}" rel="bookmark" title="Permalink to {{ article.title}}">{{ article.title }}</a></h2> </header>
+        <header> <h2 class="entry-title"><a href="{{ pagename }}" rel="bookmark" title="Permalink to {{ article.title}}">{{ article.title }}</a></h2> </header>
         <footer class="post-info">
                 <abbr class="published" title="{{ article.date.isoformat() }}">
                         {{ article.locale_date }}