diff --git a/pandas/core/reshape/merge.py b/pandas/core/reshape/merge.py
index c301d6e7c7155..d532306bc01ab 100644
--- a/pandas/core/reshape/merge.py
+++ b/pandas/core/reshape/merge.py
@@ -606,10 +606,19 @@ def __init__(
                 f"right_index parameter must be of type bool, not {type(right_index)}"
             )
 
-        # warn user when merging between different levels
+        # warn users when merging between different index levels
+        if _left.index.nlevels != _right.index.nlevels:
+            msg = (
+                "merging between different index levels can give an unintended "
+                f"result ({left.index.nlevels} levels on the left,"
+                f"{right.index.nlevels} on the right)"
+            )
+            warnings.warn(msg, UserWarning)
+
+        # warn user when merging between different column levels
         if _left.columns.nlevels != _right.columns.nlevels:
             msg = (
-                "merging between different levels can give an unintended "
+                "merging between different column levels can give an unintended "
                 f"result ({left.columns.nlevels} levels on the left,"
                 f"{right.columns.nlevels} on the right)"
             )
diff --git a/pandas/tests/frame/test_axis_select_reindex.py b/pandas/tests/frame/test_axis_select_reindex.py
index 7effa98fd8213..c6ea895191cbf 100644
--- a/pandas/tests/frame/test_axis_select_reindex.py
+++ b/pandas/tests/frame/test_axis_select_reindex.py
@@ -182,6 +182,32 @@ def test_drop_api_equivalence(self):
         with pytest.raises(ValueError):
             df.drop(axis=1)
 
+    def test_merge_join_different_index_levels(self):
+        #GH 13094
+
+        df1 = DataFrame([[2, 3], [5, 7]], columns=['a', 'p']).set_index('a')
+
+        df2 = DataFrame([[1, 2, 3], [3, 4, 8], [5, 6, 9]],
+            columns=['a', 'b', 'c']).set_index(['a', 'b'])
+
+        # join
+        columns = ['a', 'b', 'p', 'c']
+        expected = DataFrame([[5, 6, 7, 9]], columns=columns).set_index(['a', 'b'])
+
+        with tm.assert_produces_warning(UserWarning):
+            result = df1.join(df2, how='left')
+
+        tm.assert_frame_equal(result, expected)
+
+        # merge
+        columns = ['a', 'p', 'c']
+        expected = DataFrame([[5, 7, 9]], columns=columns).set_index('a')
+
+        with tm.assert_produces_warning(UserWarning):
+            result = pd.merge(df1, df2, on='a')
+        
+        tm.assert_frame_equal(result, expected)
+
     def test_merge_join_different_levels(self):
         # GH 9455