The court upheld the ruling that Microsoft had abused its dominant market position.
A probe concluded in 2004 that Microsoft was guilty of freezing out rivals in server software and products such as media players.
It was ordered to change its business and fined 497m euros (£343m; $690m).
Microsoft has now been ordered to pay 80% of the Commission's legal costs, while the Commission has to carry a specific part of Microsoft's costs.
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