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I changed a lot on my website and I want to know if this affects the Google ranking negatively.

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It will "change it a lot"! –  Marco Demaio Jun 21 '12 at 12:27

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I'll base my answer on the title of your question and assume you've changed the URLs/link structure of your website.

If you haven't done 301 redirects from the old URLs to the new URLs you've basically committed SEO suicide. You're essentially starting from scratch SEO wise by doing this. You need to do 301 redirects from the old URLs to the new URLs. That way all of the links and any rankings Google has assigned to your pages will be "transferred" to your new pages and preserving your rankings.

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Yes, i changed some of the URL structure. I made a 301 redirect but the Googles webmaster tools still shows some problems. –  Julian Jun 21 '12 at 16:15

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