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Assuming you aren’t running on a CDN or aren’t serving your JS from a separate sub-domain or server, it will load synchronously and force your HTML content to wait until it has downloaded the files. By placing the JS at the bottom of your page before the closing
I want to bring update to this topic, google has recently introduced async snipped http://support.google.com/analytics/bin/answer.py?hl=en&answer=1008080&rd=1 which can be added for your site to bring e.g. google statistics support. It should be placed bottom of the
<head> section for best performance. The point is that this increases likely hood of tracking beacon to be sent before user leaves the page.
Also it should be located there if you want to verify your site in google webmaster tools using your google analytics.
Taken from Demian Labs.
Placing scripts at the bottom of the element improves the display speed, because script compilation slows down the display.
It’s advisable to put all inline scripts at the end to improve performance, you don’t want your users to be staring at a blank white screen while the script renders. You can use defer attribute eg. to prevent link scripts from delaying your html rendering.