<ajaxtoolkit:ajaxfileupload id="AjaxFileUpload1" xmlns:ajaxtoolkit="#unknown">
ThrobberID="myThrobber"
ContextKeys="fred"
AllowedFileTypes="jpg,pdf"
MaximumNumberOfFiles=10
runat="server"/></ajaxtoolkit:ajaxfileupload>
set AllowedFileTypes as pdf,try it