Does your homepage have multiple URL’s? Do these different URLs take users to the homepage:
Are all of these versions indexed in Google? To find out, do a site: query to find them. The Google search query looks like this, site:www.mysite.com
The problem is that this is considered duplicate content. Google and other search engines view 2 different URL’s as 2 different pages. This causes the issue of duplicate content.
Another huge potential problem is that incoming links are split up among multiple URLs.
If this is the case, you should use a tool like Open Site Explorer to check the amount of linkjuice each version has, and choose the strongest to 301-redirect all versions of the homepage to. In most cases it’s the www.mysite.com version.
The 301 redirect tells the crawler that the page has permanently moved. All link juice is transferred. This is the best method to resolve the homepage canonical issue.
Once it has been implemented, you can use a HTTP Header Status Checker to confirm if it is redirecting properly. Perhaps the programmer accidently made it 302 redirect? Good to use this to confirm.
In addition, it would be good insurance to login to Google Webmaster Tools to set a “preferred domain”.
As long as we’re on the topic of using the Canonical Tag….There is another great use for the Canonical tag. It’s when ecommerce sites have an affiliate program and give all their affiliates a specific ID. In this scenerio, there could be hundreds or thousands of versions of a URL, all pointing to the same landing page.
In a nutshell, the problem is: Inbound links all linking to the same webpage, but using affiliate ID’s.
The Solution: Use a Canonical Tag to preserve the inbound link credit and site reputation.
The following URL examples would all pass link credit to the canonical URL so long as the tag is implemented within the document head: