The European Commission has fined Microsoft 899 million (£680 million) for abusing its dominant position in the market.
The penalty was imposed after the US giant failed to comply with a 2004 decision by charging unreasonable prices for access to interface documentation for work group servers, the commission said.
"Microsoft was the first company in 50 years of EU competition policy that the commission has had to fine for failure to comply with an anti-trust decision", said European competition commissioner Neelie Kroes.
In its 2004 ruling, the European Commission found Microsoft had denied rival software makers vital interoperability code which would allow their products to work with Windows.
After the ruling, Microsoft allowed access to interface documentation but demanded a royalty rate of 3.87 per cent of a licensee's product revenues for a patent licence and of 2.9 per cent for a licence giving access to the secret interoperability information.
The EU considered these prices to be too steep, and warned the company the fees breached its ruling.
Microsoft changed its fees from October 22nd 2007, giving access to the interoperability information for a flat fee of 10,000 (£7,580) and an optional worldwide patent licence for a reduced royalty of 0.4 per cent of licensees' product revenues.
The company said in a statement that the fines concerned "past issues" and it was now looking to the future.