diff --git a/autoapi/extension.py b/autoapi/extension.py
index e4361a8..32340c1 100644
--- a/autoapi/extension.py
+++ b/autoapi/extension.py
@@ -112,30 +112,39 @@ def doctree_read(app, doctree):
     """
     Inject AutoAPI into the TOC Tree dynamically.
     """
-
-    all_docs = set()
-    insert = True
     if app.env.docname == 'index':
+        all_docs = set()
+        insert = True
         nodes = doctree.traverse(toctree)
         toc_entry = '%s/index' % app.config.autoapi_root
         if not nodes:
             return
+        # Capture all existing toctree entries
         for node in nodes:
             for entry in node['entries']:
                 all_docs.add(entry[1])
-        # Don't insert if it's already present
+        # Don't insert autoapi it's already present
         for doc in all_docs:
             if doc.find(app.config.autoapi_root) != -1:
                 insert = False
         if insert and app.config.autoapi_add_toctree_entry:
-            nodes[-1]['entries'].append(
-                (None, u'%s/index' % app.config.autoapi_root)
-            )
-            nodes[-1]['includefiles'].append(u'%s/index' % app.config.autoapi_root)
-            app.info(bold('[AutoAPI] ') +
-                     darkgreen('Adding AutoAPI TOCTree [%s] to index.rst' % toc_entry)
-                     )
-            if sphinx.version_info >= (1, 5):
+            if app.config.autoapi_add_api_root_toctree:
+                # Insert full API TOC in root TOC
+                for path in app.env.autoapi_toc_entries:
+                    nodes[-1]['entries'].append(
+                        (None, path[1:])
+                    )
+                    nodes[-1]['includefiles'].append(path)
+            else:
+                # Insert AutoAPI index
+                nodes[-1]['entries'].append(
+                    (None, u'%s/index' % app.config.autoapi_root)
+                )
+                nodes[-1]['includefiles'].append(u'%s/index' % app.config.autoapi_root)
+                app.info(bold('[AutoAPI] ') +
+                         darkgreen('Adding AutoAPI TOCTree [%s] to index.rst' % toc_entry)
+                         )
+            if sphinx.version_info > (1, 5):
                 app.env.toctree.process_doc(app.env.docname, doctree)
             else:
                 app.env.build_toc_from(app.env.docname, doctree)
@@ -143,9 +152,9 @@ def doctree_read(app, doctree):
 
 def setup(app):
     app.connect('builder-inited', run_autoapi)
-    app.connect('build-finished', build_finished)
     app.connect('doctree-read', doctree_read)
     app.connect('doctree-resolved', add_domain_to_toctree)
+    app.connect('build-finished', build_finished)
     app.add_config_value('autoapi_type', 'python', 'html')
     app.add_config_value('autoapi_root', API_ROOT, 'html')
     app.add_config_value('autoapi_ignore', [], 'html')
@@ -154,6 +163,7 @@ def setup(app):
     app.add_config_value('autoapi_dirs', [], 'html')
     app.add_config_value('autoapi_keep_files', False, 'html')
     app.add_config_value('autoapi_add_toctree_entry', True, 'html')
+    app.add_config_value('autoapi_add_api_root_toctree', False, 'html')
     app.add_config_value('autoapi_template_dir', [], 'html')
     app.add_stylesheet('autoapi.css')
     directives.register_directive('autoapi-nested-parse', NestedParse)
diff --git a/autoapi/mappers/base.py b/autoapi/mappers/base.py
index 6ec0dc4..4b5d23b 100644
--- a/autoapi/mappers/base.py
+++ b/autoapi/mappers/base.py
@@ -288,6 +288,10 @@ class SphinxMapperBase(object):
         # Render Top Index
         top_level_index = os.path.join(root, 'index.rst')
         pages = self.objects.values()
+        self.app.env.autoapi_toc_entries = []
+        for page in pages:
+            if page.top_level_object:
+                self.app.env.autoapi_toc_entries.append(page.include_path)
         with open(top_level_index, 'w+') as top_level_file:
             content = self.jinja_env.get_template('index.rst')
-            top_level_file.write(content.render(pages=pages))
+            top_level_file.write(content.render(pages=self.app.env.autoapi_toc_entries))