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I have many Google Custom Search engines that I need to track. In other words, I need to know the search terms of the users. Otherwise, it is hard to improve the engines. How can I do it?

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If you're using Google Analytics, you could enable "Site Search":

Google Help : How do I set up Site Search for my profile?


Edit:

Here is a tutorial: Know What Your Customers Want: Analyze Internal Search Data With Google Analytics

On Step 6 it's important that you enter this exact formula into the Field A -> Extract A field:

q=([^&]*)&sa=Search.

Screenshot Google Analytics

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I did it, but I have a google CSE in iFrame and a standard engine from Google Sites. It does not track the Google CSE in iFrame, but it tracks the standard engine in Google Sites. I have no idea how to track the Google CSE. – hhh Jun 27 '09 at 19:13
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If the results page of your Google CSE is on your site, you can just analyze your access logs to pull the search terms out. You should see URLs like http://yoursite.com/cseresults.html?q=keywords.

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