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I think I understand the basic case for using rel="canonical": to tell Google which is the preferred URI when the same page/content may be accessed via more than one URI.

This helps you avoid duplicate content penalties. But what else does it do?

Does it also affect search ranking? i.e. will the page I specify in the canonical be ranked higher than the others? (if all else equal).

And in the case of PDF documents, I understand that you can now specify rel="canonical" for them too, using HTTP headers (i.e. in htaccess). Again, this would obviously help avoid duplicate content penalties if the PDF content is the same as the HTML page or if it can be accessed in more than one place. But does it affect ranking? or are there any other benefits to doing this.

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The ranking benefit is essentially that you prevent duplication. For example, you have a page of content, example.com/page, but for whatever reason, the same page exists with parameters, e.g., example.com/page?param=123.

The fist is crawled, indexed and ranked because your site navigation links to it. The parameter isn't linked to, but is produced when the user interacts with the page in some way. Now, if that user decides to tweet that URL or link to it from their site, you stand a good chance of getting that second URL indexed, and therefore having a duplicate page accruing SEO value.

So the total possible value of that page is split across 2 locations, which means neither has its full potential value. By using a canonical link element, you can ask search engines to index only what you regard as the canonical version – example.com/page, since that's the one you link to on your site – and attribute any backlinks, PageRank, what have you, to that canonical version.

So "will the page I specify in the canonical be ranked higher than the others?". Yes. In fact, if it's working properly, the others won't be returned in search results at all. So it's not just about duplicate content penalties, it's about concentrating the value accrued by your content onto a single, "correct" location.

Do note, though, that at least as far as Google is concerned, the canonical link element is not a directive. It's only a request, and if their algorithm decides there's some reason to ignore it, it can.

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