diff --git a/specreduce/extract.py b/specreduce/extract.py
index 62d28bd5..e1a07684 100644
--- a/specreduce/extract.py
+++ b/specreduce/extract.py
@@ -353,6 +353,10 @@ def __call__(self, image=None, trace_object=None,
         if np.any(variance < 0):
             raise ValueError("variance must be fully positive")
 
+        if np.any(np.isnan(variance)):
+            # exclude these elements by editing the input mask
+            img.mask[np.isnan(variance)] = True
+
         if np.any(variance == 0):
             # exclude these elements by editing the input mask
             img.mask[variance == 0] = True