diff --git a/CHANGES b/CHANGES
index 03e8ebe62..1be7c2c43 100644
--- a/CHANGES
+++ b/CHANGES
@@ -8,6 +8,7 @@ Bugs fixed
 * #2295: Avoid mutating dictionary errors while enumerating members in autodoc
   with Python 3
 * #2291: Fix pdflatex "Counter too large" error from footnotes inside tables of contents
+* #2292: Fix some footnotes disappear from LaTeX output
 
 
 Release 1.3.5 (released Jan 24, 2016)
diff --git a/sphinx/writers/latex.py b/sphinx/writers/latex.py
index 434d8a699..31189c7da 100644
--- a/sphinx/writers/latex.py
+++ b/sphinx/writers/latex.py
@@ -199,9 +199,14 @@ class ShowUrlsTransform(object):
         def is_auto_footnote(node):
             return isinstance(node, nodes.footnote) and node.get('auto')
 
-        def footnote_ref_by(ids):
+        def footnote_ref_by(node):
+            ids = node['ids']
+            parent = list(traverse_parent(node, (nodes.document, addnodes.start_of_file)))[0]
+
             def is_footnote_ref(node):
-                return isinstance(node, nodes.footnote_reference) and ids[0] == node['refid']
+                return (isinstance(node, nodes.footnote_reference) and
+                        ids[0] == node['refid'] and
+                        parent in list(traverse_parent(node)))
 
             return is_footnote_ref
 
@@ -220,7 +225,7 @@ class ShowUrlsTransform(object):
                 footnote['names'].remove(old_label)
             footnote['names'].append(label)
 
-            for footnote_ref in self.document.traverse(footnote_ref_by(footnote['ids'])):
+            for footnote_ref in self.document.traverse(footnote_ref_by(footnote)):
                 footnote_ref.remove(footnote_ref[0])
                 footnote_ref += nodes.Text(label)
 
diff --git a/tests/roots/test-footnotes/bar.rst b/tests/roots/test-footnotes/bar.rst
new file mode 100644
index 000000000..660c66306
--- /dev/null
+++ b/tests/roots/test-footnotes/bar.rst
@@ -0,0 +1,6 @@
+bar
+===
+
+Same footnote number [1]_ in bar.rst
+
+.. [1] footnote in bar
diff --git a/tests/roots/test-footnotes/baz.rst b/tests/roots/test-footnotes/baz.rst
new file mode 100644
index 000000000..af496c5f6
--- /dev/null
+++ b/tests/roots/test-footnotes/baz.rst
@@ -0,0 +1,6 @@
+baz
+===
+
+Auto footnote number [#]_ in baz.rst
+
+.. [#] footnote in baz
diff --git a/tests/roots/test-footnotes/index.rst b/tests/roots/test-footnotes/index.rst
index 228fccf8d..3a8bc25c5 100644
--- a/tests/roots/test-footnotes/index.rst
+++ b/tests/roots/test-footnotes/index.rst
@@ -2,6 +2,11 @@
 test-footenotes
 ===============
 
+.. toctree::
+
+   bar
+   baz
+
 .. contents::
    :local:
 
diff --git a/tests/test_build_latex.py b/tests/test_build_latex.py
index 4533ee4c0..c4a887d44 100644
--- a/tests/test_build_latex.py
+++ b/tests/test_build_latex.py
@@ -372,6 +372,8 @@ def test_latex_show_urls_is_inline(app, status, warning):
     print(result)
     print(status.getvalue())
     print(warning.getvalue())
+    assert 'Same footnote number \\footnote[1]{\nfootnote in bar\n} in bar.rst' in result
+    assert 'Auto footnote number \\footnote[1]{\nfootnote in baz\n} in baz.rst' in result
     assert ('\\phantomsection\\label{index:id26}{\\hyperref[index:the\\string-section'
             '\\string-with\\string-a\\string-reference\\string-to\\string-authoryear]'
             '{\\emph{The section with a reference to \\phantomsection\\label{index:id1}'
@@ -405,6 +407,8 @@ def test_latex_show_urls_is_footnote(app, status, warning):
     print(result)
     print(status.getvalue())
     print(warning.getvalue())
+    assert 'Same footnote number \\footnote[1]{\nfootnote in bar\n} in bar.rst' in result
+    assert 'Auto footnote number \\footnote[2]{\nfootnote in baz\n} in baz.rst' in result
     assert ('\\phantomsection\\label{index:id26}{\\hyperref[index:the\\string-section'
             '\\string-with\\string-a\\string-reference\\string-to\\string-authoryear]'
             '{\\emph{The section with a reference to \\phantomsection\\label{index:id1}'
@@ -412,20 +416,20 @@ def test_latex_show_urls_is_footnote(app, status, warning):
     assert ('\\phantomsection\\label{index:id27}{\\hyperref[index:the\\string-section'
             '\\string-with\\string-a\\string-reference\\string-to]{\\emph{The section '
             'with a reference to }}}' in result)
-    assert 'First footnote: \\footnote[2]{\nFirst\n}' in result
+    assert 'First footnote: \\footnote[3]{\nFirst\n}' in result
     assert 'Second footnote: \\footnote[1]{\nSecond\n}' in result
     assert ('\\href{http://sphinx-doc.org/}{Sphinx}'
-            '\\footnote[3]{\nhttp://sphinx-doc.org/\n}' in result)
-    assert 'Third footnote: \\footnote[5]{\nThird\n}' in result
+            '\\footnote[4]{\nhttp://sphinx-doc.org/\n}' in result)
+    assert 'Third footnote: \\footnote[6]{\nThird\n}' in result
     assert ('\\href{http://sphinx-doc.org/~test/}{URL including tilde}'
-            '\\footnote[4]{\nhttp://sphinx-doc.org/\\textasciitilde{}test/\n}' in result)
-    assert ('\\item[{\\href{http://sphinx-doc.org/}{URL in term}\\protect\\footnotemark[7]}] '
-            '\\leavevmode\\footnotetext[7]{\nhttp://sphinx-doc.org/\n}\nDescription' in result)
-    assert ('\\item[{Footnote in term \\protect\\footnotemark[9]}] '
-            '\\leavevmode\\footnotetext[9]{\nFootnote in term\n}\nDescription' in result)
-    assert ('\\item[{\\href{http://sphinx-doc.org/}{Term in deflist}\\protect'
-            '\\footnotemark[8]}] '
+            '\\footnote[5]{\nhttp://sphinx-doc.org/\\textasciitilde{}test/\n}' in result)
+    assert ('\\item[{\\href{http://sphinx-doc.org/}{URL in term}\\protect\\footnotemark[8]}] '
             '\\leavevmode\\footnotetext[8]{\nhttp://sphinx-doc.org/\n}\nDescription' in result)
+    assert ('\\item[{Footnote in term \\protect\\footnotemark[10]}] '
+            '\\leavevmode\\footnotetext[10]{\nFootnote in term\n}\nDescription' in result)
+    assert ('\\item[{\\href{http://sphinx-doc.org/}{Term in deflist}\\protect'
+            '\\footnotemark[9]}] '
+            '\\leavevmode\\footnotetext[9]{\nhttp://sphinx-doc.org/\n}\nDescription' in result)
     assert ('\\href{https://github.com/sphinx-doc/sphinx}'
             '{https://github.com/sphinx-doc/sphinx}\n' in result)
     assert ('\\href{mailto:sphinx-dev@googlegroups.com}'
@@ -440,6 +444,8 @@ def test_latex_show_urls_is_no(app, status, warning):
     print(result)
     print(status.getvalue())
     print(warning.getvalue())
+    assert 'Same footnote number \\footnote[1]{\nfootnote in bar\n} in bar.rst' in result
+    assert 'Auto footnote number \\footnote[1]{\nfootnote in baz\n} in baz.rst' in result
     assert ('\\phantomsection\\label{index:id26}{\\hyperref[index:the\\string-section'
             '\\string-with\\string-a\\string-reference\\string-to\\string-authoryear]'
             '{\\emph{The section with a reference to \\phantomsection\\label{index:id1}'