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We have multiple websites, each site servers number of countries, and we used to have Geo-Ip Auto redirect system (no one likes auto-redirect), so we implemented another redirect system also uses Geo-IP database, but showing a pop-up window (HTML layer pop-up, so it can't be rejected), this window asks the visitor if he would like to continue with this page or go to the correct website of his country. We also added a test line before showing the pop-up, so if the visitor is Googlebot, the popup will not show up :).

I was wondering if this effects our websites SEO?

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The popup will never "show" to the search engine bots anyway. Bots simply read the HTML of the page, and don't execute any JavaScript at all (not strictly true, however good enough for this point).

If your popup window's HTML is on the page without using JavaScript, the search engine bot will read it and consider it part of your page.

However, this will make very minimal/no effect on your search engine rankings.

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  • Google, does and can execute and render javascript on a page.
    – Anagio
    Sep 17, 2013 at 21:58
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    Read again: "not strictly true, however good enough for this point". Google does parse Javascript in order to find links to other pages/websites and to detect common cloaking methods, however it doesn't execute all Javascript on a page. Sep 18, 2013 at 10:23
  • I didn't use Javascript at all, Its purely html, & I have excluded the googlebot too.
    – Joseph
    Sep 19, 2013 at 7:29

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