diff --git a/doc/source/whatsnew/v0.21.0.txt b/doc/source/whatsnew/v0.21.0.txt
index fcadd26156b1d4..942e37a29f8d57 100644
--- a/doc/source/whatsnew/v0.21.0.txt
+++ b/doc/source/whatsnew/v0.21.0.txt
@@ -358,6 +358,7 @@ Indexing
 - Allow unicode empty strings as placeholders in multilevel columns in Python 2 (:issue:`17099`)
 - Bug in ``.iloc`` when used with inplace addition or assignment and an int indexer on a ``MultiIndex`` causing the wrong indexes to be read from and written to (:issue:`17148`)
 - Bug in ``.isin()`` in which checking membership in empty ``Series`` objects raised an error (:issue:`16991`)
+- Bug in ``CategoricalIndex`` reindexing in which specified indices containing duplicates were not being respected (:issue:`17323`)
 
 I/O
 ^^^
diff --git a/pandas/core/indexes/category.py b/pandas/core/indexes/category.py
index f22407308e0944..0681202289311e 100644
--- a/pandas/core/indexes/category.py
+++ b/pandas/core/indexes/category.py
@@ -487,7 +487,7 @@ def get_indexer(self, target, method=None, limit=None, tolerance=None):
         method = missing.clean_reindex_fill_method(method)
         target = ibase._ensure_index(target)
 
-        if self.equals(target):
+        if self.is_unique and self.equals(target):
             return np.arange(len(self), dtype='intp')
 
         if method == 'pad' or method == 'backfill':
diff --git a/pandas/tests/indexes/test_category.py b/pandas/tests/indexes/test_category.py
index 64bd6df361aeb7..3a1efced81a0ea 100644
--- a/pandas/tests/indexes/test_category.py
+++ b/pandas/tests/indexes/test_category.py
@@ -365,29 +365,36 @@ def test_astype(self):
         tm.assert_index_equal(result, expected)
 
     def test_reindex_base(self):
-
-        # determined by cat ordering
-        idx = self.create_index()
+        # Determined by cat ordering.
+        idx = CategoricalIndex(list("cab"), categories=list("cab"))
         expected = np.arange(len(idx), dtype=np.intp)
 
         actual = idx.get_indexer(idx)
         tm.assert_numpy_array_equal(expected, actual)
 
-        with tm.assert_raises_regex(ValueError, 'Invalid fill method'):
-            idx.get_indexer(idx, method='invalid')
+        with tm.assert_raises_regex(ValueError, "Invalid fill method"):
+            idx.get_indexer(idx, method="invalid")
 
     def test_reindexing(self):
+        np.random.seed(123456789)
 
         ci = self.create_index()
         oidx = Index(np.array(ci))
 
-        for n in [1, 2, 5, len(ci)]:
+        for n in [1, 2, 5]:
             finder = oidx[np.random.randint(0, len(ci), size=n)]
             expected = oidx.get_indexer_non_unique(finder)[0]
 
             actual = ci.get_indexer(finder)
             tm.assert_numpy_array_equal(expected, actual)
 
+        # see gh-17323
+        for finder in [list("aabbca"), list("aababca")]:
+            expected = oidx.get_indexer_non_unique(finder)[0]
+
+            actual = ci.get_indexer(finder)
+            tm.assert_numpy_array_equal(expected, actual)
+
     def test_reindex_dtype(self):
         c = CategoricalIndex(['a', 'b', 'c', 'a'])
         res, indexer = c.reindex(['a', 'c'])