The first will look at whether Microsoft unfairly ties its Explorer internet browser to its Windows operating system.
In a parallel probe, the Commission will look at the interoperability of Microsoft software with rival products.
The firm said it would cooperate with the latest enquiry. In October, the EU ruled that the firm broke antitrust rules.
"This initiation of proceedings does not imply that the Commission has proof of an infringement," said the Commission in a statement.
"It only signifies that the Commission will further investigate the case as a matter of priority."
The latest investigation by the Commission comes after two complaints, one by Norwegian company Opera, the other by pan-European software-makers group European Committee for Interoperable Systems.
The move by the Commission's competition officials will stoke the flames of a long-running battle between
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