diff --git a/IPython/core/shellapp.py b/IPython/core/shellapp.py
index 24f6825..f46a0e5 100644
--- a/IPython/core/shellapp.py
+++ b/IPython/core/shellapp.py
@@ -287,16 +287,19 @@ class InteractiveShellApp(Configurable):
         self._run_startup_files()
         self._run_exec_lines()
         self._run_exec_files()
+        
+        # Hide variables defined here from %who etc.
+        if self.hide_initial_ns:
+            self.shell.user_ns_hidden.update(self.shell.user_ns)
+        
+        # command-line execution (ipython -i script.py, ipython -m module)
+        # should *not* be excluded from %whos
         self._run_cmd_line_code()
         self._run_module()
         
         # flush output, so itwon't be attached to the first cell
         sys.stdout.flush()
         sys.stderr.flush()
-        
-        # Hide variables defined here from %who etc.
-        if self.hide_initial_ns:
-            self.shell.user_ns_hidden.update(self.shell.user_ns)
 
     def _run_exec_lines(self):
         """Run lines of code in IPythonApp.exec_lines in the user's namespace."""