Check this sample. First click Set to set hidden field server side and then click get button
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<title></title>
<script type="text/javascript" language="javascript">
function Get() {
alert(document.getElementById("<%=HiddenField1.ClientID %>").value);
}
</script>
</head>
<body>
<form id="form1" runat="server">
<asp:ScriptManager ID="ScriptManager1" runat="server">
</asp:ScriptManager>
<asp:UpdatePanel ID="UpdatePanel1" runat="server">
<ContentTemplate>
<asp:Button ID="Button1" runat="server" Text="Set" onclick="Button1_Click" />
<asp:HiddenField ID="HiddenField1" runat="server" />
</ContentTemplate>
</asp:UpdatePanel>
<input id="Button2" type="button" value="Get" onclick = "Get()" />
</form>
</body>
</html>
Code
protected void Button1_Click(object sender, EventArgs e)
{
HiddenField1.Value = "TRUE";
}