diff -r 6ad256175971 Lib/idlelib/PyShell.py
--- a/Lib/idlelib/PyShell.py	Sun Mar 31 15:56:02 2013 -0500
+++ b/Lib/idlelib/PyShell.py	Sun Mar 31 17:44:37 2013 -0500
@@ -446,6 +446,9 @@
         self.terminate_subprocess()
         console = self.tkconsole
         was_executing = console.executing
+        if console.reading:
+            console.endoffile = True
+            console.top.quit()
         console.executing = False
         self.spawn_subprocess()
         try:
@@ -967,10 +970,10 @@
                 parent=self.text)
             if response is False:
                 return "cancel"
+        self.canceled = True
+        self.closing = True
         if self.reading:
             self.top.quit()
-        self.canceled = True
-        self.closing = True
         # Wait for poll_subprocess() rescheduling to stop
         self.text.after(2 * self.pollinterval, self.close2)
 
@@ -1033,6 +1036,8 @@
             self.top.mainloop()  # nested mainloop()
         finally:
             self.reading = save
+        if self.closing:
+            return "" # return EOF for the closing process
         line = self.text.get("iomark", "end-1c")
         if len(line) == 0:  # may be EOF if we quit our mainloop with Ctrl-C
             line = "\n"