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When you say external cdn, is it a cdn that you control or a public repository? If you control the cdn and you are just using it to open more channels for the browser download I would recommend setting the link in the header. From there you can set the canonical tag of the resource in the header. Here is a screenshot of the http request of my logo on my site, http://screencast.com/t/rQoiVIo8deZ5  It is getting the file from the cdn, but it is also telling search engines that the canonical location of the file is on my domain. This is something Google has supported for a while now, http://googlewebmastercentral.blogspot.com/2011/06/supporting-relcanonical-http-headers.html If you are using a public repository, you do not have control over the header, so I would not worry too much about it.