Why doesn’t the clickthrough data in Webmaster Tools match what I see in Google Analytics?

Matt's answer:

Today we’ve got a question from Paul in Washington, D.C. Paul wants to know, why doesn’t the click through data for the keywords in my webmaster portal report match my Google Analytics data? It’s a very good question. So, just to give you a little bit of perspective, the Google Analytics team is separate from the Google webmaster tools team. And in fact, they’re in different locations, they use different code bases. They’re really sort of completely different silos within Google, so it’s not as if a ton of data sharing goes on between those two areas of Google. I’ll give you one example way in which they can be skewed. Google webmaster report — the webmaster portal report — essentially might say, look, we know the number of impressions, we know the number of clicks, or whatever, because that’s monitoring stuff on the server side of Google. It’s basically saying, ok, we know how many times people saw this particular website. Google Analytics uses JavaScript, so if someone has JavaScript turned off or they’re using a browser which does not have very good JavaScript support, maybe it’s an ancient browser or something like that, or maybe they’re using no script and they don’t trust JavaScript to run, and they’ve disabled Google Analytics for whatever reason. That user is going to look relatively invisible to Google Analytics. So JavaScript is just one example way where you might look in your server logs, you might look in the Google webmaster tools report, or you might look in Google Analytics. And you might see slightly different numbers there, but to a first approximation, they should be quite close. You can always use slightly different methodologies, and that can give you a little bit different numbers. It would be nice if things were completely unified and they were counted exactly the same. But you’re always going to have a few situations like people who disable JavaScript deliberately or people who, for whatever reason, have JavaScript turned off. And that might skew your results no matter what. So we figured it’s better to give you as good information as we have in both cases, on both situations, and then you can take that data, consider the source, and then still get good, useful, actionable information out of it.

by Matt Cutts - Google's Head of Search Quality Team

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