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Basically, the way the development of a site I am working on has happened, virtually all pages use H2 instead of H1 as the "root" title (and then H3-5 are used appropriately).

Since Google pays such special attention to headings as part of structure, will this affect my search engine rankings?

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up vote 10 down vote accepted

Yes, it does matter. According to the google webmaster blog,

The lower the number on your heading tag, the more important the text, in the eyes of Google and your users.

So, to tell google that the title is important, you should mark it up with an <h1> tag instead of an <h2> tag, which is considered less important to google.

Edit: the SEOMoz search engine ranking factors might be of interest to people who want to know more about how headers impact search engine rankings.

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Straight from the horse's mouth ... they even describe my situation. I better get to it then. Thanks. –  Alex Feb 5 '12 at 15:12
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Good find. I would add that while in order it's more important - the degree of importance is hard to define. –  Mike Hudson Feb 5 '12 at 22:26
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@Christofian: cool link! –  Marco Demaio Feb 7 '12 at 19:30
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Short answer, it matters, yes (but how much is questionable).

Have a read of this article dmystifying H Tags by Sean Anderson at hobo web and a it's also worth reading this thread on the subject at submit express.

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