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We need more details. What do you have open? What browser/OS are you using? What sites are they? Have you checked for spyware yet? There's a tutorial on removing spyware in the Tech Institute I wrote, try that and see if it helps.
If you are using IExplore, then the problem is spyware. I had the same problem. Use Firefox! http://www.mozilla.com/firefox
It has a built-in pop-up blocker and, IT's FREE!!