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When I check Google Index > Content Keywords in Google Webmaster Tools, it shows lots of unimportant keywords like: to, is, are, from, in, on, we, you and etc.

That's very natural these words are found more than others because it's so hard to find a sentence without one of these popular words.

I'm wondering why Google is doing this? Does it make a problem for SEO? How to deal with that?

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At what position in the list do these keywords appear? Is your site entirely English? – w3dk Mar 19 '14 at 23:45
@W3d No, my the website contents are not in English. I mentioned some similar keywords. These keywords are on the top (1-8). – Omid Amraei Mar 20 '14 at 15:41
This looks like it might be language specific? On English sites I have never seen these "unimportant keywords" (aka. stop words), such as the ones you mention, listed under Content Keywords in GWT. – w3dk Mar 20 '14 at 19:44
Are you using two different languages on the same page? This might cause it to happen, when Google thinks the page is in one language. I would recommend you create separate pages for each language, if this is possible. – Michael Hampton May 9 '14 at 20:35
@MichaelHampton I have a Persian (Farsi) page. However, there are some (maybe 1 or 2) English words in each page. – Omid Amraei May 10 '14 at 10:43

It does not indicate an SEO problem when common words appear in the content keywords list. I have a multi-language website for which I have each language verified as a separate site. I only see common stop words appearing in the list (is, a, the, etc) for some of the languages.

Google does not intend this list as a list of keywords for which you are likely to rank in the search results. Rather it is a hacked site prevention measure. If you see keywords like "viagra" or "sex" appearing in the list then you will know that malware is serving those terms to Googlebot.

Having words that you actually use on your site appear high in this list is never a problem. Even when those words are not important words.

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