Last year Google added support for canonical tags in HTTP headers.
You can view the headers which are normally invisible by using a HTTP viewing tool such as Rex Swain, Web Sniffer or a local application like Fiddler.
HTTP/1.1·200·OK
Date:·Tue,·24·Jul·2012·20:23:29·GMT
Server:·Apache/2.2.16·(Unix)·mod_ssl/2.2.16·OpenSSL/0.9.8e-fips-rhel5·DAV/2·mod_auth_passthrough/2.1·mod_bwlimited/1.4·FrontPage/5.0.2.2635·mod_perl/2.0.4·Perl/v5.8.8(CR)(LF)
X-Powered-By:·PHP/5.2.9
Vary:·Cookie
Link: <http://blog.semetrical.com/>; rel=”canonical”
X-Pingback:·http://blog.semetrical.com/xmlrpc.php
WP-Super-Cache:·Served·legacy·cache·file
Connection:·close
Transfer-Encoding:·chunked
Content-Type:·text/html;·charset=UTF-8
As with normal canonical tag implementations, you need to make sure your canonical URLs are correct.
We have now added support to DeepCrawl, our site architecture analysis tool. DeepCrawl identifies all pages on your site where the canonical tag URL is different to the actual URL and puts them in a report so you can audit them.