The sites being targeted are Bolt.com and Grouper.com. Universal said it plans to seek damages of $150,000 for each incident of copyright infringement as well as damages.
Universal, whose artists include U2 and Mariah Carey, said that the sites "cannot reasonably expect to build their business on the backs of our content and the hard work of our artists and songwriters without permission and without compensating the content creators".
It is the first time a label has sued one of the video-sharing websites, although such a move had long been expected. Before Universal's deal with YouTube, the record company had threatened to sue it as well. Now YouTube has permission to show thousands of videos legally, paying a fee to Universal and with a promise to filter out unauthorised Universal content.
Sites such as YouTube, which was bought by Google in a $1.6bn share deal last week, present a dilemma for entertainment companies. While they are aware of the potential for promoting their music and films, and wary of generating bad publicity by suing sites that are hugely popular, they are searching for a way to make money from the video-sharing phenomenon.
Bolt.com's homepage carried a message from one of its owners, Jay Gould, regarding the lawsuit. It said: "We understand the love you have for your favourite musical artists, but Bolt respects the rights of copyright owners such as Universal Music and their artists, and we ask that you please do so as well by not uploading their videos to Bolt."
Grouper, which was acquired by Universal rival Sony Pictures in August, has not yet responded on its site, although chief executive Josh Felser is quoted in the Financial Times saying that the lawsuit "is without merit and we expect to prevail".
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