You can hook up a handler to the shown event on the modalpopup that allows you to set the focus: 

function pageLoad()
{
    var popup = $find('ModalPopupClientID');
    popup.add_shown(SetFocus);
}

function SetFocus()
{
    $get('TextBoxClientID').focus();
}

Note that the ModalPopupExtender has a BehaviorID property to give you a javascript object handle:

    <ajx:ModalPopupExtender
        ID="ModalWin_Extender"  
        BehaviorID="ModalWin_Extender_ClientObject"
        TargetControlID="lnkNull" 
        PopupControlID="ModalWin"
        runat="server">
    </ajx:ModalPopupExtender>

You then hook up the Client Object's shown() handler to the function of your choice:

 
$find('ModalWin_Extender_ClientObject').add_shown(jsYourFunction);

 

Oh and by the way - server-side, you can set control focus using this:

ScriptManager.GetCurrent(this.Page).SetFocus(txtMyTextBox);

zootius:

 

You then hook up the Client Object's shown() handler to the function of your choice:

 
$find('ModalWin_Extender_ClientObject').add_shown(jsYourFunction);

 

where do I have to insert this line? In the body: onload() event? 

Jason's right. Took me a while to realise this too, but Ajax.Net registers some new client-side event handlers, so if you have a javascript function called pageLoad(), it gets called automatically after Ajax.net has finished doing its own onLoad stuff.

More info here: http://ajax.asp.net/docs/overview/AJAXClientEvents.aspx 

This works perfect for me.

Thank you very much 

 I'm having a problem getting this to work, I've tried it and I get an error message.

 Error : Can't move focus to the control because it is invisble, not enabled, or of a type that does not accept focus.

Here is my code,

<script type="text/javascript">


Sys.Application.add_load(modalSetup);
function SetFocusOnControl()
{
    // set the focus with javascript, e.g.: window.getElementById("xyz").focus();
    document.getElementById("txt1").focus();
}
function modalSetup()
{
    var modalPopup = $find('popup1');             // <. this is the BehaviorID from the ModalPopupExtender
    modalPopup.add_showing(SetFocusOnControl);          
}
<asp:Button ID="btn1" runat="server" Width="80px" CausesValidation="false"
                    Text=" Swipe Card " Visible="false" />  <asp:Button ID="btnManual" runat="server"
                        Width="90px" Text=" Manual Entry " Visible="false" />               
                <ajaxToolkit:ModalPopupExtender ID="popup1" runat="server" TargetControlID="btn1"
                    PopupControlID="pnl1" BackgroundCssClass="modalBackground" DropShadow="true" BehaviorID="popup1" />
<asp:Panel ID="pnl1" runat="server" CssClass="modalPopup" style="display:none;" Width="310">
        <table cellpadding="1" cellspacing="0" width="300" border="0" align="center">						
				<tr>
					<td>
						<textarea rows="1" cols="10" id="txt1" onkeyup="CheckSwipe();" style="color:White;scrollbar-base-color: #FFFFFF;" class="hiddenScrollbars"></textarea>
					</td>					
				</tr>
				
			</table>
</asp:Panel>

Try using:

modalPopup.add_shown(SetFocusOnControl);

This will fire your function *after* the modalpopup is shown.

Thanks, I got it to work. Now I have another problem though. When my popup is shown I have some javascript that runs. The first time it runs fine, but if you hide the popup and show it again and try to run the javascript again it does not run. I don't get any script errors and the script will work fine on a page without the modal popup. Any ideas?