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You should be able to do this with an image.
If in you opener window you defined an image using:
<script language="JavaScript"><!--
if (document.images)
var myUniqueReference = new Image();
//--></script>Then in the popup window you should be able to detect this using:
<script language="JavaScript"><!--
if (opener.myUniqueReference ? true : false)
alert('My window');
else
alert('Not my window');
//--></script>This should work even if the opener now contains a document from another server.