Thanks!
I got everything to work using RegisterClientScriptInclude but the only way I could get it to work was calling RegisterStartupScript again when I wanted to call the function. It works great but I wanted to make sure I was doing it correctly or if there was a better way to call my function without using RegisterStartupScript. Is there a better way to do this than the way I'm dooing it?
Thanks
GEM

Javascript code:
Code:
//// Jscript.js /////
function openNewWin2(url) {
    var x = new Object;
    x = window.open(url, 'mynewwin', 'width=600,height=600,toolbar=1');
}
HTML Code:
<%@ Page Language="VB" AutoEventWireup="false" CodeFile="Default2.aspx.vb" Inherits="Default2" %>
<!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">
<script language="javascript" type="text/javascript" src="JScript.js"  ></script>
<head runat="server">
    <title></title>
</head>
<body>
    <form id="form1" runat="server">
    <div>
          <asp:Button ID="btnOpenPop" runat="server" Text="Open Pop"  />
    </div>
    </form>
</body>
</html>
Code:
Protected Sub Page_Load(ByVal sender As Object, ByVal e As System.EventArgs) Handles Me.Load
        If Not IsPostBack Then
            Page.ClientScript.RegisterClientScriptInclude("Java1", ResolveClientUrl("Jscript.js"))
        End If
    End Sub

    Protected Sub btnOpenPop_Click(ByVal sender As Object, ByVal e As System.EventArgs) Handles btnOpenPop.Click
        Dim url As String = "http://www.yahoo.com"
        ClientScript.RegisterStartupScript(Me.GetType(), "OpenWin", "<script>openNewWin2('" & url & "')</script>")
        '\\is there a better way to call my function than using RegisterStartupScript - this seem rendundant
    End Sub