diff --git a/RELEASE.rst b/RELEASE.rst
index b88580bdf2aa1..c9508c6a47e73 100644
--- a/RELEASE.rst
+++ b/RELEASE.rst
@@ -39,6 +39,7 @@ pandas 0.9.0
 
 **Improvements to existing features**
 
+  - Proper handling of NA values in merge operations (#1990)
   - Add ``flags`` option for ``re.compile`` in some Series.str methods (#1659)
   - Parsing of UTC date strings in read_* functions (#1693)
   - Handle generator input to Series (#1679)
diff --git a/pandas/tools/merge.py b/pandas/tools/merge.py
index d64d79913b10f..4a50016c39927 100644
--- a/pandas/tools/merge.py
+++ b/pandas/tools/merge.py
@@ -142,7 +142,6 @@ def _merger(x, y):
 
 
 
-# TODO: NA group handling
 # TODO: transformations??
 # TODO: only copy DataFrames when modification necessary
 
@@ -572,7 +571,16 @@ def _factorize_keys(lk, rk, sort=True):
     if sort:
         llab, rlab = _sort_labels(rizer.uniques, llab, rlab)
 
-        # TODO: na handling
+    # NA group
+    lmask = llab == -1; lany = lmask.any()
+    rmask = rlab == -1; rany = rmask.any()
+
+    if lany or rany:
+        if lany:
+            np.putmask(llab, lmask, count)
+        if rany:
+            np.putmask(rlab, rmask, count)
+        count += 1
 
     return llab, rlab, count
 
diff --git a/pandas/tools/tests/test_merge.py b/pandas/tools/tests/test_merge.py
index 829471deb9e6d..d7ad584e8f62f 100644
--- a/pandas/tools/tests/test_merge.py
+++ b/pandas/tools/tests/test_merge.py
@@ -777,6 +777,34 @@ def test_left_merge_na_buglet(self):
         expected = left.join(rdf)
         tm.assert_frame_equal(merged, expected)
 
+    def test_merge_na_keys(self):
+        data = [[1950, "A", 1.5],
+                [1950, "B", 1.5],
+                [1955, "B", 1.5],
+                [1960, "B", np.nan],
+                [1970, "B", 4.],
+                [1950, "C", 4.],
+                [1960, "C", np.nan],
+                [1965, "C", 3.],
+                [1970, "C", 4.]]
+
+        frame = DataFrame(data, columns=["year", "panel", "data"])
+
+        other_data = [[1960, 'A', np.nan],
+                      [1970, 'A', np.nan],
+                      [1955, 'A', np.nan],
+                      [1965, 'A', np.nan],
+                      [1965, 'B', np.nan],
+                      [1955, 'C', np.nan]]
+        other = DataFrame(other_data, columns=['year', 'panel', 'data'])
+
+        result = frame.merge(other, how='outer')
+
+        expected = frame.fillna(-999).merge(other.fillna(-999), how='outer')
+        expected = expected.replace(-999, np.nan)
+
+        tm.assert_frame_equal(result, expected)
+
 
 def _check_join(left, right, result, join_col, how='left',
                 lsuffix='_x', rsuffix='_y'):
diff --git a/setup.py b/setup.py
index a91a3b63181f8..67cd8e8aad43e 100755
--- a/setup.py
+++ b/setup.py
@@ -372,8 +372,7 @@ def srcpath(name=None, suffix='.pyx', subdir='src'):
 
 algos_ext = Extension('pandas._algos',
                       sources=[srcpath('generated', suffix=suffix)],
-                      include_dirs=[np.get_include()],
-                      )
+                      include_dirs=[np.get_include()])
 
 lib_depends = tseries_depends + ['pandas/src/numpy_helper.h',
                                  'pandas/src/datetime/np_datetime.h',