diff --git a/lib/iris/analysis/stats.py b/lib/iris/analysis/stats.py
index f3715f6e8b..3d16b2018e 100644
--- a/lib/iris/analysis/stats.py
+++ b/lib/iris/analysis/stats.py
@@ -1,4 +1,4 @@
-# (C) British Crown Copyright 2013 - 2014, Met Office
+# (C) British Crown Copyright 2013 - 2015, Met Office
 #
 # This file is part of Iris.
 #
@@ -30,7 +30,8 @@ def _get_calc_view(cube_a, cube_b, corr_coords):
     """
     This function takes two cubes and returns cubes which are
     flattened so that efficient comparisons can be performed
-    between the two.
+    between the two. If the arrays are maksed then only values
+    that are unmasked in both arrays are used.
 
     Args:
 
@@ -94,7 +95,29 @@ def _get_calc_view(cube_a, cube_b, corr_coords):
     reshaped_b = data_b.transpose(slice_ind+res_ind)\
                        .reshape(dim_i_len, dim_j_len)
 
-    return reshaped_a, reshaped_b, res_ind
+    # Remove data where one or both cubes are masked
+    # First deal with the case that either cube is unmasked
+    # Collapse masks to the dimension we are correlating over (0th)
+    if np.ma.is_masked(reshaped_a):
+        a_not_masked = np.logical_not(reshaped_a.mask).any(axis=1)
+    else:
+        a_not_masked = True
+    if np.ma.is_masked(reshaped_b):
+        b_not_masked = np.logical_not(reshaped_b.mask.any(axis=1))
+    else:
+        b_not_masked = True
+
+    both_not_masked = a_not_masked & b_not_masked
+    try:
+        # compress to good values using mask array
+        return_a = reshaped_a.compress(both_not_masked)
+        return_b = reshaped_b.compress(both_not_masked)
+    except ValueError:
+        # expect when masks are just non-array True/False
+        return_a = reshaped_a
+        return_b = reshaped_b
+
+    return return_a, return_b, res_ind
 
 
 def pearsonr(cube_a, cube_b, corr_coords=None):
diff --git a/lib/iris/tests/analysis/test_stats.py b/lib/iris/tests/analysis/test_stats.py
index 992978530c..3c12509fb2 100644
--- a/lib/iris/tests/analysis/test_stats.py
+++ b/lib/iris/tests/analysis/test_stats.py
@@ -1,4 +1,4 @@
-# (C) British Crown Copyright 2014, Met Office
+# (C) British Crown Copyright 2014 - 2015, Met Office
 #
 # This file is part of Iris.
 #
@@ -39,6 +39,14 @@ def setUp(self):
         self.cube_b = iris.load_cube(iris.sample_data_path('GloSea4',
                                                            'ensemble_002.pp'))
 
+        dummycrd = iris.coords.DimCoord(range(100), long_name="dummy")
+        mask_a = [True]*20 + [False]*80
+        self.masked_a = iris.cube.Cube(np.ma.masked_array(range(100), mask_a))
+        self.masked_a.add_dim_coord(dummycrd, 0)
+        mask_b = [False]*10 + [True]*20 + [False]*70
+        self.masked_b = iris.cube.Cube(np.ma.masked_array(range(100), mask_b))
+        self.masked_b.add_dim_coord(dummycrd, 0)
+
     def test_perfect_corr(self):
         r = stats.pearsonr(self.cube_a, self.cube_a,
                            ['latitude',   'longitude'])
@@ -101,6 +109,24 @@ def test_non_existent_coord(self):
         with self.assertRaises(ValueError):
             stats.pearsonr(self.cube_a, self.cube_b, 'bad_coord')
 
+    def test_differing_masks(self):
+        """
+        Test that we only consider points
+        where both cubes are unmasked
+
+        """
+        r = stats.pearsonr(self.masked_a, self.masked_b)
+        self.assertArrayEqual(r.data, [1.0])
+
+        self.masked_a.data.mask = True
+        r = stats.pearsonr(self.masked_a, self.masked_b)
+        self.assertArrayEqual(r.data.mask, [True])
+
+        self.masked_a.data.mask = True
+        self.masked_b.data.mask = True
+        r = stats.pearsonr(self.masked_a, self.masked_b)
+        self.assertArrayEqual(r.data.mask, [True])
+
 
 if __name__ == '__main__':
     tests.main()