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I was observing Google results for months to determine if pop-up ads have a negative impact on SEO. Regarding my observations, sites without pop-ups usually get ranked better. Actually, that doesn't really prove anything since most of sites without pop-ups have better content too!

Anyways, does anyone know the effect of using pop-ups in regards to SEO? Can Google or other search engines find out if your site uses pop-up ads? Do they run java scripts for this purpose?

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According to a Matt Cutts 2012 post, sites with a lot of ads "above-the-fold", meaning before the content, can be penalized. However, a normal amount of ads and a content rich site won't suffer.

However, they recently made updates for mobile search and said to avoid download apps pop-ups or you'll lose mobile search rankings.

Reference : http://googlewebmastercentral.blogspot.com/2012/01/page-layout-algorithm-improvement.html

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Welcome to the site! It helps to add a link to the reference you're citing so that others can review and learn from them too (and usually just takes a quick search). –  dan Nov 25 '13 at 12:56
    
In the article Matt Cutts talks about above-the-fold ads. How about pop ads!? –  Pazis Nov 25 '13 at 16:26
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Google can parse JavaScript and they might find out if you're using popups. But it's possible that they don't figure it out everytime.

My belief is that Google doesn't like popups and might penalize a website for using them.

Lately I barely find any website with popups in the search results. Are you sure you aren't talking about modals?

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