Microsoft CEO Steve Ballmer has said that every user of the open source Linux system could owe his company money for using its intellectual property. The statement will confirm the worst fears of the open source community.

Microsoft recently signed a deal for SUSE Linux, a Novell-owned distribution of the Linux operating system. The two companies pledged that they would improve the interoperability of their products. Open source advocates were amazed at the deal, but Ballmer's comments could vindicate the suspicions of some.

Ballmer said in a question and answer session at a technology conference that Microsoft signed the deal because Linux "uses our intellectual property" and it wanted to "get the appropriate economic return for our shareholders from our innovation".

Those claims to rights in Linux will set alarm bells ringing in the open source community. Some had argued that the deal was a sophisticated way of claiming rights over the software.

The deal involved a payment of $440m from Microsoft to Novell for coupons which Microsoft users can redeem against support for SUSE Linux. A payment that now looks to be more important, though, is a $40m payment from Novell to Microsoft, reported to be a pledge that Microsoft will not sue its users for patent infringement.

Ballmer was explaining the rationale behind that deal. "Novell pays us some money for the right to tell customers that anybody who uses SUSE Linux is appropriately covered," he said, according to Computerworld. "This is important to us, because we believe every Linux customer basically has an undisclosed balance sheet liability."

The comments will provoke fury amongst open source advocates who believe that Microsoft has no claims at all on the intellectual property contained in Linux.

In explaining the deal before Ballmer's comments, Roger Levy, vice-president of open platform solutions at Novell, told a Paris press conference that the deal solved a problem which was costing both firms money.

"Customers were afraid they'd get sued if they crossed platforms and this meant that they were hesitating on buying decisions," said Levy. "As part of the deal Microsoft will agree not to sue our customers and we agreed not to sue their customers. This is not an agreement between companies – we can still sue each other for any number of reasons – but ultimately our respective customers needed peace of mind to make decisions."

Red Hat, which also distributes commercial versions of Linux, refused to sign a similar deal with Microsoft. Red Hat "does not believe there is a need for or basis for the type of relationship defined in the Microsoft-Novell announcement", deputy general counsel Mark Webbink told news agency Bloomberg in a statement.

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