diff --git a/cleanup.py b/cleanup.py
new file mode 100644
index 0000000..9a1b811
--- /dev/null
+++ b/cleanup.py
@@ -0,0 +1,98 @@
+#!/usr/bin/env python
+"""
+Cleanup for Singularity container
+
+Scan the images in the singularity CVMFS.  If an image directory has not been "linked" to for 2 days, 
+remove the image directory.
+
+Maintains state in a file in the root singularity directory named .missing_links.json
+
+"""
+import glob
+import os
+import json
+import shutil
+import argparse
+import time
+from datetime import datetime, timedelta
+
+SINGULARITY_BASE = '/cvmfs/singularity.opensciencegrid.org'
+
+# /cvmfs/singularity.opensciencegrid.org/.missing_links.json
+JSON_LOCATION = os.path.join(SINGULARITY_BASE, '.missing_links.json')
+
+# JSON structure:
+# {
+#   "missing_links": {
+#       "/cvmfs/singularity.opensciencegrid.org/.images/7d/ba009871baa50e01d655a80f79728800401bbd0f5e7e18b5055839e713c09f": "<timestamp_last_linked>"
+#       ...
+#   }
+# }
+
+def cleanup(delay=2, test=False):
+    '''Clean up unlinked singularity images'''
+    # Read in the old json, if it exists
+    json_missing_links = {}
+    try:
+        with open(JSON_LOCATION) as json_file:
+            json_missing_links = json.load(json_file)['missing_links']
+    except (IOError, ValueError):
+        # File is missing, unreadable, or damaged
+        pass
+
+    # Get all the images in the repo
+
+    # Walk the directory /cvmfs/singularity.opensciencegrid.org/.images/*
+    image_dirs = glob.glob(os.path.join(SINGULARITY_BASE, '.images/*/*'))
+
+    # Walk the named image dirs
+    named_image_dir = glob.glob(os.path.join(SINGULARITY_BASE, '*/*'))
+
+    # For named image dir, look at the what the symlink points at 
+    for named_image in named_image_dir:
+        link_target = os.readlink(named_image)
+        while link_target in image_dirs:
+            image_dirs.remove(link_target)
+        # Remove linked image from json (in case link is restored)
+        json_missing_links.pop(link_target, None)
+
+    # Now, for each image, see if it's in the json
+    for image_dir in image_dirs:
+        if image_dir not in json_missing_links:
+            # Add it to the json
+            print("Newly found missing link: %s" % (image_dir))
+            json_missing_links[image_dir] = int(time.time())
+
+    # Loop through the json missing links, removing directories if over the `delay` days
+    expiry = datetime.now() - timedelta(days=delay)
+    for image_dir, last_linked in json_missing_links.items():
+        date_last_linked = datetime.fromtimestamp(last_linked)
+        if date_last_linked < expiry:
+            # Confirm that we're inside the managed directory
+            if not image_dir.startswith(SINGULARITY_BASE):
+                continue
+            # Remove the directory
+            print("Removing missing link: %s" % image_dir)
+            if not test:
+                shutil.rmtree(image_dir)
+                del json_missing_links[image_dir]
+
+    # Write out the end json
+    with open(JSON_LOCATION, 'w') as json_file:
+        json.dump({"missing_links": json_missing_links}, json_file)
+
+def main():
+    '''Main function'''
+    args = parse_args()
+    cleanup(test=args.test)
+
+def parse_args():
+    '''Parse CLI options'''
+    parser = argparse.ArgumentParser()
+
+    parser.add_argument('--test', action='store_true',
+                        help="Don't remove files, but go through the motions of removing them.")
+    return parser.parse_args()
+
+if __name__ == "__main__":
+    main()
diff --git a/cvmfs-singularity-sync b/cvmfs-singularity-sync
index 6794b30..64af204 100755
--- a/cvmfs-singularity-sync
+++ b/cvmfs-singularity-sync
@@ -43,6 +43,7 @@ import urllib2
 import hashlib
 import tempfile
 import tarfile
+import cleanup
 
 def main():
     parser = argparse.ArgumentParser(description="Bootstrap Docker images for Singularity containers deployed to CVMFS")
@@ -129,6 +130,7 @@ def main():
                 if retval:
                     final_retval = retval
         print "All requested images have been attempted; final return code: %d" % final_retval
+        cleanup.cleanup()
         return final_retval