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I want to display a JavaScript popup when visitors access my website, however I believe Google will decrease my rankings when they detect a popup. So, is there any way to hide a JavaScript popup for Googlebot, or another way to display a popup without affecting my rankings?

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Never treat Googlebot any different than your real users

Google's bots that visit your site should be treated just as any other user and therefor attempting to hide content can actually harm your website. Google treats hiding of content as cloaking and is against their rules and if detected you can expect a heavy slap.

Many websites have popups on visit

You shouldn't assume any popup will harm your rankings if that popup is useful to the users visiting your site. Many sites these days have popups i.e groupon, holiday bookings and so forth...

The right popups

As long as your using friendly popups that do not open 'browser windows' with a nasty iframe or confirm to leave page then the popup should be ok...

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