diff --git a/src/rsatoolbox/rdm/compare.py b/src/rsatoolbox/rdm/compare.py
index 3d7f8420..a6253c76 100644
--- a/src/rsatoolbox/rdm/compare.py
+++ b/src/rsatoolbox/rdm/compare.py
@@ -671,12 +671,14 @@ def _parse_input_rdms(rdm1, rdm2):
             vector2 = rdm2
     if not vector1.shape[1] == vector2.shape[1]:
         raise ValueError('rdm1 and rdm2 must be RDMs of equal shape')
-    nan_idx = ~np.isnan(vector1)
-    vector1_no_nan = vector1[nan_idx].reshape(vector1.shape[0], -1)
-    vector2_no_nan = vector2[~np.isnan(vector2)].reshape(vector2.shape[0], -1)
-    if not vector1_no_nan.shape[1] == vector2_no_nan.shape[1]:
+    # A NaN in any RDM means that position must be excluded from all
+    nan_mask = ~np.isnan(vector1).any(axis=0)
+    if not np.all(nan_mask == ~np.isnan(vector2).any(axis=0)):
+        # Only raise error when rdm1 and rdm2 conflict
         raise ValueError('rdm1 and rdm2 have different nan positions')
-    return vector1_no_nan, vector2_no_nan, nan_idx[0]
+    vector1_no_nan = vector1[:,nan_mask].reshape(vector1.shape[0], -1)
+    vector2_no_nan = vector2[:,nan_mask].reshape(vector2.shape[0], -1)
+    return vector1_no_nan, vector2_no_nan, nan_mask
 
 
 def _sq_bures_metric_first_way(A, B):