diff --git a/flags.py b/flags.py
index 3ee07390b19e5d64f742ff26ca22be6d18eedf95..0da9372ce52c572a7f8d9c592bf9f91eb63c490f 100644
--- a/flags.py
+++ b/flags.py
@@ -3,3 +3,4 @@
 INVALID = 1
 LOW = 2
 HIGH = 4
+MISSING = 8
diff --git a/modis2airs_collect.py b/modis2airs_collect.py
index 2106ef4a14fbdfb65afe331714af8b49604197b0..ee1d863584e65036cdbec88673470067977889b0 100644
--- a/modis2airs_collect.py
+++ b/modis2airs_collect.py
@@ -1,6 +1,7 @@
 import numpy
 import sys
 
+from flags import *
 from modis_bright import modis_bright
 from pyhdf.SD import SD, SDC
 from util import HdfWriter
@@ -47,12 +48,13 @@ bt_mean[:] = modis_bright(rad_mean)
 std_bt[:] = modis_bright(rad_mean + rad_std) - bt_mean
 
 # for any pixel where N is zero, use fill values for the other
-# variables
+# variables and set the MISSING flag
 missing_idxs = (n == 0)
 rad_mean[missing_idxs] = -9999.0
 rad_std[missing_idxs] = -9999.0
 bt_mean[missing_idxs] = -9999.0
 std_bt[missing_idxs] = -9999.0
+flags[missing_idxs] = MISSING
 
 # output to HDF
 writer = HdfWriter(output_file)