What sort of pop-ups? Are these system pop-ups or advertising pop-ups? Do they only appear when you're using an Internet Browser or are they constant?
If they're advertising pop-ups then first scan your system for Spyware; use either Spybot Search and Destroy or Ad-aware (don't use the host resident parts - its not worth it).
If it's only when you're browsing, try changing your browser to something not Internet Explorer, either Firefox or Opera (my favourite).
dave, November 2008
