I love using a small pop-ups, to sign up for email newsletters, on pages where I have users engaged and I'm not worried about ranking on that specific page. I know Matt Cutts indicated in a video that to the best of his knowledge Google doesn't take Pop-ups or pop-unders into consideration. But just about everywhere I go SEOers are saying that pop-ups and pop-unders hurt rankings? My question is if I only have these pop-ups on a few pages of my site where I'm not worried about ranking them, will it hurt rankings of any other pages? Curious to see what you guys think.
Pop-up and similar kind won't hurt your ranking directly but may be indirectly. 1. Most of pop-up seems annoying for most peoples, even for a newsletter sign up. That could cause a no linking to from some link sources 2. As #1 said, it could also caused an almost instantly turned back after a few second visited your website. Most of "instant turned back" might influence Google to think something wrong may going on with your website by tracked on visitor behavior and activities
Pop-ups or pop-unders might not be very bad from SEO perspectives but since nowadays most of such unwanted advertising packages get blocked automatically and instantly by the browsing tools, so it is recommended not using them on the homepages. Besides, you do not need them to develop a professional website as there are numerous other ways to tell people what points are covered on your site.
Popups probably don't hurt your rankings as it's outside of the meta information: titles/descrip/tags, but it will effect your Bounce rate negatively. Many people are turned off by these popups and will quickly close out the site upon seeing them.
The ones that really hurt you are the ones that won't let the visitor do anything until they answer the question "OK" or "Cancel."