diff --git a/CHANGES b/CHANGES
index c8b08a6fd..9b9b30018 100644
--- a/CHANGES
+++ b/CHANGES
@@ -35,6 +35,8 @@ Incompatible changes
 * Footer "Continued on next page" of LaTeX longtable's now not framed (refs: #3497)
 * #3529: The arguments of ``BuildEnvironment.__init__`` is changed
 * #3082: Use latexmk for pdf (and dvi) targets (Unix-like platforms only)
+* #3558: Emit warnings if footnotes and citations are not referenced.  The
+  warnings can be suppressed by ``suppress_warnings``.
 
 Features removed
 ----------------
diff --git a/doc/config.rst b/doc/config.rst
index 15a9a339b..3bc6bebb7 100644
--- a/doc/config.rst
+++ b/doc/config.rst
@@ -236,6 +236,7 @@ General configuration
    * ref.keyword
    * ref.option
    * ref.citation
+   * ref.footnote
    * ref.doc
    * misc.highlighting_failure
    * toc.secnum
@@ -255,6 +256,10 @@ General configuration
 
       Added ``epub.unknown_project_files``
 
+   .. versionchanged:: 1.6
+
+      Added ``ref.footnote``
+
 .. confval:: needs_sphinx
 
    If set to a ``major.minor`` version string like ``'1.1'``, Sphinx will
diff --git a/sphinx/io.py b/sphinx/io.py
index 2e1e25599..636167332 100644
--- a/sphinx/io.py
+++ b/sphinx/io.py
@@ -18,6 +18,7 @@ from sphinx.transforms import (
     ApplySourceWorkaround, ExtraTranslatableNodes, CitationReferences,
     DefaultSubstitutions, MoveModuleTargets, HandleCodeBlocks, SortIds,
     AutoNumbering, AutoIndexUpgrader, FilterSystemMessages,
+    UnreferencedFootnotesDetector
 )
 from sphinx.transforms.compact_bullet_list import RefOnlyBulletListTransform
 from sphinx.transforms.i18n import (
@@ -92,7 +93,7 @@ class SphinxStandaloneReader(SphinxBaseReader):
                   Locale, CitationReferences, DefaultSubstitutions, MoveModuleTargets,
                   HandleCodeBlocks, AutoNumbering, AutoIndexUpgrader, SortIds,
                   RemoveTranslatableInline, PreserveTranslatableMessages, FilterSystemMessages,
-                  RefOnlyBulletListTransform]
+                  RefOnlyBulletListTransform, UnreferencedFootnotesDetector]
 
 
 class SphinxI18nReader(SphinxBaseReader):
@@ -106,7 +107,8 @@ class SphinxI18nReader(SphinxBaseReader):
     transforms = [ApplySourceWorkaround, ExtraTranslatableNodes, CitationReferences,
                   DefaultSubstitutions, MoveModuleTargets, HandleCodeBlocks,
                   AutoNumbering, SortIds, RemoveTranslatableInline,
-                  FilterSystemMessages, RefOnlyBulletListTransform]
+                  FilterSystemMessages, RefOnlyBulletListTransform,
+                  UnreferencedFootnotesDetector]
 
     def __init__(self, *args, **kwargs):
         # type: (Any, Any) -> None
diff --git a/sphinx/transforms/__init__.py b/sphinx/transforms/__init__.py
index b7306bb2d..bfe52413f 100644
--- a/sphinx/transforms/__init__.py
+++ b/sphinx/transforms/__init__.py
@@ -277,6 +277,32 @@ class ExtraTranslatableNodes(SphinxTransform):
             node['translatable'] = True
 
 
+class UnreferencedFootnotesDetector(SphinxTransform):
+    """
+    detect unreferenced footnotes and citations, and emit warnings
+    """
+    default_priority = 200
+
+    def apply(self):
+        for node in self.document.footnotes:
+            if node['names'][0] not in self.document.footnote_refs:
+                logger.warning('Footnote [%s] is not referenced.', node['names'][0],
+                               type='ref', subtype='footnote',
+                               location=node)
+
+        for node in self.document.autofootnotes:
+            if not any(ref['auto'] == node['auto'] for ref in self.document.autofootnote_refs):
+                logger.warning('Footnote [#] is not referenced.',
+                               type='ref', subtype='footnote',
+                               location=node)
+
+        for node in self.document.citations:
+            if node['names'][0] not in self.document.citation_refs:
+                logger.warning('Citation [%s] is not referenced.', node['names'][0],
+                               type='ref', subtype='citation',
+                               location=node)
+
+
 class FilterSystemMessages(SphinxTransform):
     """Filter system messages from a doctree."""
     default_priority = 999