Pop up Ads can be very annoying and a lot of blogs use this to chase potential fans away. Pop up ads coming up when the visitor has reached a certain part of the page won’t be that bad, but the one that comes up each time a page is opened is as bad as using a mega phone to draw the attention of a customer sleeping in your reception.
Pop up ads are even a red flag according to Adsense policy. Most bloggers use Adsense and if you read through their Dos and Don’ts, you will find a limitation to the use of Pop ups.
If you need to draw attention, try keeping the content of a pop up just above the fold, in a dark background, and then make sure the height of the box is big enough that the reader does not see any part of the page’s content. But let the reader know that he or she can scroll down to read the content of the page. At least, this won’t come as a surprise to the visitor and there will be no need to click on anything to close the pop up.
Another solution is to do this exact thing, but place the box just below the content.