diff --git a/CHANGES b/CHANGES
index b47d08966..c37a72f73 100644
--- a/CHANGES
+++ b/CHANGES
@@ -9,6 +9,7 @@ Bugs fixed
 * #2882: Fall back to a GET request on 403 status in linkcheck
 * #2902: jsdump.loads fails to load search index if keywords starts with
   underscore
+* #2900: Fix epub content.opf: add auto generated orphan files to spine.
 
 Release 1.4.6 (released Aug 20, 2016)
 =====================================
diff --git a/sphinx/builders/epub.py b/sphinx/builders/epub.py
index f5f0d8098..e2c780261 100644
--- a/sphinx/builders/epub.py
+++ b/sphinx/builders/epub.py
@@ -123,6 +123,9 @@ FILE_TEMPLATE = u'''\
 SPINE_TEMPLATE = u'''\
     <itemref idref="%(idref)s" />'''
 
+NO_LINEAR_SPINE_TEMPLATE = u'''\
+    <itemref idref="%(idref)s" linear="no" />'''
+
 GUIDE_TEMPLATE = u'''\
     <reference type="%(type)s" title="%(title)s" href="%(uri)s" />'''
 
@@ -202,6 +205,7 @@ class EpubBuilder(StandaloneHTMLBuilder):
     coverpage_name = COVERPAGE_NAME
     file_template = FILE_TEMPLATE
     spine_template = SPINE_TEMPLATE
+    no_linear_spine_template = NO_LINEAR_SPINE_TEMPLATE
     guide_template = GUIDE_TEMPLATE
     toctree_template = TOCTREE_TEMPLATE
     doctype = DOCTYPE
@@ -584,6 +588,7 @@ class EpubBuilder(StandaloneHTMLBuilder):
 
         # spine
         spine = []
+        spinefiles = set()
         for item in self.refnodes:
             if '#' in item['refuri']:
                 continue
@@ -592,14 +597,23 @@ class EpubBuilder(StandaloneHTMLBuilder):
             spine.append(self.spine_template % {
                 'idref': self.esc(self.make_id(item['refuri']))
             })
+            spinefiles.add(item['refuri'])
         for info in self.domain_indices:
             spine.append(self.spine_template % {
                 'idref': self.esc(self.make_id(info[0] + self.out_suffix))
             })
+            spinefiles.add(info[0] + self.out_suffix)
         if self.get_builder_config('use_index', 'epub'):
             spine.append(self.spine_template % {
                 'idref': self.esc(self.make_id('genindex' + self.out_suffix))
             })
+            spinefiles.add('genindex' + self.out_suffix)
+        # add auto generated files
+        for name in self.files:
+            if name not in spinefiles and name.endswith(self.out_suffix):
+                spine.append(self.no_linear_spine_template % {
+                    'idref': self.esc(self.make_id(name))
+                })
 
         # add the optional cover
         content_tmpl = self.content_template
@@ -626,6 +640,7 @@ class EpubBuilder(StandaloneHTMLBuilder):
                 ctx = {'image': self.esc(image), 'title': self.config.project}
                 self.handle_page(
                     path.splitext(self.coverpage_name)[0], ctx, html_tmpl)
+                spinefiles.add(self.coverpage_name)
 
         guide = []
         auto_add_cover = True