diff --git a/pandas/core/format.py b/pandas/core/format.py
index 5062fd9be6357..ae0d95b1c3074 100644
--- a/pandas/core/format.py
+++ b/pandas/core/format.py
@@ -1393,8 +1393,12 @@ def _format_regular_rows(self):
             for idx, idxval in enumerate(index_values):
                 yield ExcelCell(self.rowcounter + idx, 0, idxval, header_style)
 
+        # Get a frame that will account for any duplicates in the column names.
+        col_mapped_frame = self.df.loc[:, self.columns]
+
+        # Write the body of the frame data series by series.
         for colidx in range(len(self.columns)):
-            series = self.df.iloc[:, colidx]
+            series = col_mapped_frame.iloc[:, colidx]
             for i, val in enumerate(series):
                 yield ExcelCell(self.rowcounter + i, colidx + coloffset, val)
 
@@ -1461,8 +1465,12 @@ def _format_hierarchical_rows(self):
                                         header_style)
                     gcolidx += 1
 
+        # Get a frame that will account for any duplicates in the column names.
+        col_mapped_frame = self.df.loc[:, self.columns]
+
+        # Write the body of the frame data series by series.
         for colidx in range(len(self.columns)):
-            series = self.df.iloc[:, colidx]
+            series = col_mapped_frame.iloc[:, colidx]
             for i, val in enumerate(series):
                 yield ExcelCell(self.rowcounter + i, gcolidx + colidx, val)
 
diff --git a/pandas/io/tests/test_excel.py b/pandas/io/tests/test_excel.py
index 8bcf5e461ce7c..a126bd965e4b6 100644
--- a/pandas/io/tests/test_excel.py
+++ b/pandas/io/tests/test_excel.py
@@ -922,11 +922,25 @@ def test_duplicated_columns(self):
             write_frame.columns = colnames
             write_frame.to_excel(path, 'test1')
 
-            read_frame = read_excel(path, 'test1').astype(np.int64)
+            read_frame = read_excel(path, 'test1')
             read_frame.columns = colnames
 
             tm.assert_frame_equal(write_frame, read_frame)
 
+    def test_swapped_columns(self):
+        # Test for issue #5427.
+        _skip_if_no_xlrd()
+
+        with ensure_clean(self.ext) as path:
+            write_frame = DataFrame({'A': [1, 1, 1],
+                                     'B': [2, 2, 2]})
+            write_frame.to_excel(path, 'test1', cols=['B', 'A'])
+
+            read_frame = read_excel(path, 'test1', header=0)
+
+            tm.assert_series_equal(write_frame['A'], read_frame['A'])
+            tm.assert_series_equal(write_frame['B'], read_frame['B'])
+
 
 class OpenpyxlTests(ExcelWriterBase, unittest.TestCase):
     ext = '.xlsx'