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This is something that can cause headache for many webmasters. Yes, there’s some search engine penalty if your website got hacked.

It’s increasing day by day and I found some comments on a YouTube video from the webmasters who got hacked recently.

Hacking

mfdotcom
I had a site running the previous version of Wordpress where a hacker injected code to show a 301 permanent redirect to the GoogleBot, but normal visitors were not affected and shown the site normally.
It screwed search rankings for awhile, but was fixed soon enough and oddly Google didn’t notice.

OldWelshGuy
I have seen a few sites that were hacked to serve PRN, and got seriously slapped. down. Many have bounced back real quick 9as we caught them early enough), but others where the site owners didn’t click what the problem was for loss of traffic (and sales) took months.

When a hacker hack a website, they usually put some malicious codes in the source codes of the website. When search engines crawl that page and found that malicious code in the webpage, they treat is as SPAM and threat to the visitors, you get the penalty. This is also applicable if the hacker put some redirection or doorway pages.

What you need to do when you get hacked?
There are some steps that you must take immediately after getting hacked.

1. Change all your Passwords to something stronger.
2. Do a Google Safe Browsing Diagnosis to check if Google already picked it up. (Replace the YourDomain.com with your domain)
3. Scan your website using your hosting control panel.
4. Clean the website and remove all the unwanted files. If you are using any script, back it up completely along with the databases and delete all the files. Then make a clean reinstall and restore the databases.
5. Scan your site again to check if any threats left.
6. Delete the old Sitemap and generate a new one. Then submit it again.
7. Place a reconsideration request from the Google Webmaster Tools.

If you clean the website before search engines notice it, you might not receive any penalty. But, if you are late, you’ll have it. Below is a video from Matt Cutts on the penalty that you may receive for getting hacked.