/*place in app_code to use throughout your site:*/

    /// <summary>
    /// setup cGET for all Page Controls
    /// </summary>
    public static void setup_cGET(Page page)
    {
        setup_cGET(AllControls(page), page);
    }
    /// <summary>
    /// setup cGET for all items in your control
    /// </summary>
    public static void setup_cGET(Control c, Page page)
    {
        setup_cGET(AllControls(c), page);
    }
    /// <summary>
    /// setup cGET for passed Controls ex. setup_cGET(txtbox1, txtbox2...);
    /// </summary>
    public static void setup_cGET(Page page, params Control[] wc)
    {
        if (wc.Length > 0)
        {
            List<Control> r = new List<Control>();
            for (int i = 0; i < wc.Length; i++)
            {
                r.Add(wc[i]);
            }
            setup_cGET(r, page);
        }
    }
    /// <summary>
    /// Setup a javascript cGET function that looks up controls. This solves the problem of not knowing the id in c# master pages
    /// Can only run this function once, should be using a scriptmanager
    /// </summary>
    /// <param name="c"></param>
    public static void setup_cGET(List<Control> lc, Page page)
    {
        if (lc.Count <= 0)
            return;

       // Now loop through the controls and build the client and server id's
        string js = "var cGET_serverIDs = new Object();";
        foreach (Control c in lc)
        {
            if (c.ID != null && c.ID.Length > 0)
                js += "cGET_serverIDs['" + c.ID + "'] = '" + c.ClientID + "';\n";
        }
        
        // Now register the method GetClientId, used to get the client id of tthe control
        ScriptManager.RegisterStartupScript(page, page.GetType(), "cGET",
            js+
            "function cGET(serverId) " +
            "    { " +
            "       if (cGET_serverIDs[serverId] != null) " +
            "          return document.getElementById(cGET_serverIDs[serverId]);  " +
            "         " +
            "       return document.getElementById(serverId);" +
            "    } "
            , true);

    }

    /// <summary>
    /// Loads all controls recursively. 
    /// </summary>
    /// <param name="container">The container to search for the control passed. Remember
    /// all controls (Panel, GroupBox, Form, etc are all containsers for controls
    /// </param>
    /// <returns></returns>
    private static List<Control> AllControls(Control container)
    {
        List<Control> r = new List<Control>();

        foreach (Control ctrl in container.Controls)
        {
            foreach (Control c in AllControls(ctrl))
                r.Add(c);
        }

        r.Add(container);

        return r;
    }
/* on each page */
    protected void Page_Load(object sender, EventArgs e)
    {
        GlobalFunction.setup_cGET(Form, this);
}

/*.js file */
cGET('textBoxID').value = '5';

Because of master pages C# changes your id's to make them unique. This allows you to place your javascript in a seperate .js file or just get rid of a document.getElementById('<%=control.ClientID%>');type solution

c# master page document.getElementById problem

C#