The revamp of MSN Search UK - which, according to MSN figures, is visited by 13.6 million people a month - is being undertaken to offer a cleaner, more focused site.
MSN admitted the move was in part made to protect the advertising value of the lucrative paid-for search result listings.
The listings, provided by third parties including Overture Services, allow advertisers to get top-ranked search positions by paying to link to search terms that users input into the engine.
"We have done this based on user experience. The search is becoming increasingly important for us and it is all about relevance - people don't come to the search section to see advertising," Robin Kellett, the business manager of MSN Search, said. "Paid-for listings are important to us and part of this is to focus on that."
Kellett added that for now it was only MSN UK that was to ditch banner ads, but that the European operation would most likely follow suit.
The move continues the trend started by large media owners in the US, notably the MSN rival AOL and the women's portal iVillage.com, to dump intrusive ad formats such as pop-ups.