EU regulators said the company charged "unreasonable prices" until last October to software developers who wanted to make products compatible with the Windows desktop operating system.
Microsoft (MSFT, Fortune 500) immediately said that these fines were about past issues that have been resolved and the company was now working under new principles to make its products more open.
The fine is the largest ever for a single company and the first time the EU has penalized a business for failing to obey an antitrust order.
The penalty far outweighs a a March 2004 decision that fined Microsoft $613 million and ordered it to share communications information with rivals within 120 days, taking an appeal to an EU court that it lost last September.
The EU alleged that Microsoft withheld crucial interoperability information for desktop PC software - where it is the world's leading supplier - to squeeze into a new market and damage rivals that make programs for workgroup servers that help office computers connect to each other and to printers and faxes.
The company delayed complying with the EU order for three years, the EU said, only making changes on Oct. 22 to the patent licenses it charges companies that need data to help them make software that works with Microsoft.
Microsoft had initially set a royalty rate of 3.87% of a licensee's product revenues for patents and demanded that companies looking for communication information - which it said was highly secret - pay 2.98% of their products' revenues.
The EU complained last March that these rates were unfair. Under threat of fines, Microsoft two months later reduced the patent rate to 0.7% and the information license to 0.5% - but only in Europe, leaving the worldwide rates unchanged.
The EU's Court of First Instance ruling that upheld regulators' views changed the company's mind again in October when it offered a new license for interoperability information for a flat fee of $14,000 and an optional worldwide patent license for a reduced royalty of 0.4%.
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