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Either allow for the size taken up by toolbars in Internet Explorer when specifying the width and height to the window:
<script language="JavaScript"><!--
if (nagiator.appName=='Internet Explorer')
var width=100,height=150;
else
var width=100,height=100;
window.open('about.blank','windowName','width=' + width + ',height=' + height);
//--></script>Or from within the the popup window, resize it to the size you require:
<script language="JavaScript"><!--
if (document.all)
window.resizeTo(100,150);
else if (document.layers)
window.resizeTo(100,100);
}
//--></script>