The Commission said on Monday that it has opened two new probes into unfair practices by the software giant.
Microsoft has again been accused of using its dominant position to muscle out smaller vendors and block the development of compatible software.
One of the investigations concerns the ongoing interoperability case between Microsoft and the Commission.
The Commission plans to look into allegations that Microsoft has not been allowing outside vendors sufficient access to develop interoperable products.
The investigation will focus on Microsoft's Office, .Net, and server software, and seek to determine whether the new Open XML is "sufficiently interoperable" with competing office suites.
The second investigation centres on a complaint filed to the Commission by browser developer Opera.
The Norwegian company complained that Microsoft has made Internet Explorer incompatible with various open standards, effectively putting the formats at a competitive disadvantage.
Microsoft has also been accused of violating rules against the bundling of software. The Commission hopes to determine whether the bundling of services such as desktop search and Windows Live illegally take advantage of Windows' large market share.
In a statement provided to vnunet.com, Microsoft vowed to cooperate fully with the investigation.
"We are committed to ensuring that Microsoft is in full compliance with European law and our obligations as established by the European Court of First Instance in its September 2007 ruling," a spokesperson said.
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