diff --git a/gitup/config.py b/gitup/config.py
index 0e1e069..51cb4f0 100644
--- a/gitup/config.py
+++ b/gitup/config.py
@@ -37,8 +37,27 @@ def _load_config_file(config_path=None):
     except IOError:
         return []
     paths = [path.decode("utf8").strip() for path in paths]
+    paths = _strip_comment_lines(paths)
     return [path for path in paths if path]
 
+def _strip_comment_lines(paths):
+    """Remove any lines starting with #."""
+    i = 0
+    while i < len(paths):
+        path = paths[i]
+        removed_comment = False
+        for j in range(0, len(path)):
+            path_char = path[j]
+            if path_char == " ":
+                continue
+            if path_char == "#":
+                removed_comment = True
+                paths.pop(i)
+                break
+        if removed_comment is False:
+            i = i + 1
+    return paths
+
 def _save_config_file(bookmarks, config_path=None):
     """Save the bookmarks list to the given config file."""
     run_migrations()