I advise that you use the public API of the control: http://www.telerik.com/help/aspnet-ajax/window-programming-radwindow-methods.html. It offers the set_contentElement() method. Note that the ContentTemplate is designed as a container for server controls, so you would need to declare and use a RadWindow with a ContenTemplate (even blank) for this to work as expected. The ContentTemplate element is not created upon client-side setting at this point, so having a content that is not where it is supposed to be may break the control afterwards (e.g., if autosizing is used). More details are available here: http://feedback.telerik.com/Project/108/Feedback/Details/129174.
The code posted by Shinu would work with the Classic RenderMode, but would throw an error with the Lightweight mode, because there are no more tables used.
Of course, a third option is to point the RadWIndow to a page like blank.html where you can use the same approach to write manually to the document. This article explains how to call a function in the page loaded in the RadWindow so you can write to the document: http://www.telerik.com/help/aspnet-ajax/window-programming-calling-functions.html.
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